LiteFold/DisProt huggingface dataset:
Protein: DP03253 (UniProt P08799)
Region: residues 487	to 508
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
There are breaks in the polypeptide chain  between  Gln  19 and  Leu  27,  Ala  205  and  Gly  209, Phe 487 and Leu 508, Arg 620 and Asn 626, and Glu  681 and Gly 683, where the density is poorly defined.
PDB - unmodeled residues 487 - 508
Cross-references: PDB:1MND
Protein: DP03253 (UniProt P08799)
Region: residues 691	to 762
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
There are breaks in the polypeptide chain  between  Gln  19 and  Leu  27,  Ala  205  and  Gly  209, Phe 487 and Leu 508, Arg 620 and Asn 626, and Glu  681 and Gly 683, where the density is poorly defined.
PDB - unmodeled residues 691 - 762
Cross-references: PDB:1MND
Protein: DP03253 (UniProt P08799)
Region: residues 487	to 500
Annotation: order (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
 After  refinement  the final model included 743 residues
PDB - residues 487-500 ordered
Cross-references: PDB:1MMD
Protein: DP03253 (UniProt P08799)
Region: residues 691	to 759
Annotation: disorder to order (Structural transition)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
 After  refinement  the final model included 743 residues
PDB - residues 691-759 ordered
Movement of the  lower domain  relative to the  upper domain of the central  segment of the heavy chain in the MgADPAIF4S1Dc complex is coupled to a structural change in the COOH-terminal domains.
The structures of the beryllium and aluminum fluoride complexes suggest that movements in the myosin heavy chain associated with the lower domain of the central 50 kDa segment coupled to movements  in  the  COOH-terminal  segment are the primary source of this conformational change. 
Cross-references: PDB:1MMD
Protein: DP03253 (UniProt P08799)
Region: residues 702	to 719
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
PDB - unmodeled residues 702-719
It has been observed that when the c-axis shrinks below 180 Å disorder is induced into the NH2- and COOH-terminal regions of the protein.
Cross-references: PDB:1MMA
Protein: DP03253 (UniProt P08799)
Region: residues 748	to 762
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
PDB - unmodeled residues 748-752
Cross-references: PDB:1VOM
Protein: DP03254 (UniProt P52848)
Region: residues 558	to 578
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Interdomain region not visible in the crystal structure.
Cross-references: PDB:1NST
Protein: DP03254 (UniProt P52848)
Region: residues 587	to 600
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The N-terminal 18 residues (587–600) and 4 residues from 665 to 669 are disordered in the NST1 crystal.
Cross-references: PDB:1NST
Protein: DP03255 (UniProt P16035)
Region: residues 209	to 220
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
No electron density was found for the C-terminal 12 residues, indicating disorder for this part of the chain.
Cross-references: PDB:1BR9
Protein: DP03255 (UniProt P16035)
Region: residues 212	to 220
Annotation: protein binding (Molecular function)
Evidence: deletion mutation phenotypic evidence used in manual assertion
Supporting statements:
The C-terminal peptide of TIMP-2 is proposed to exist as an exposed "tail" responsible for binding to progelatinase A and for increasing the rate of inhibition of active gelatinase A through electrostatic interactions with the C-terminal domain of the enzyme. The C-terminal domains of both TIMP-1 and TIMP-2 participate in low-affinity interactions with the C-terminal domain of gelatinase A which increase the rate of association by a factor of about 100 in both cases.
The work concentrates on a kinetic analysis of factors affecting the rate of association of the inhibitors with gelatinase A and demonstrates that the C-terminal domains of both proteins play an important role in controlling the rate of reaction with active enzyme. C-Terminal domain interactions are also responsible for the binding of TIMP-2 to progelatinase A.
The C-terminal nine amino acid peptide of TIMP-2 appears to make an important contribution to the rate of reaction because when this is removed the rate constant decreases approximately 4-fold to resemble that of TIMP-1. The marked decrease in the rate of inhibition by TIMP-2 with increasing ionic strength confirms the importance of ionic interactions to its mechanism. The effect is considerably decreased with the forms of TIMP-2 that lack the C-terminal peptide and is insignificant in the case of TIMP-1. Thus, the C-terminus of TIMP-2 is primarily, although not completely, responsible for the ionic interactions with gelatinase A.
Protein: DP03255 (UniProt P16035)
Region: residues 212	to 220
Annotation: molecular function inhibitor activity (Molecular function)
Evidence: deletion mutation phenotypic evidence used in manual assertion
Supporting statements:
The C-terminal peptide of TIMP-2 is proposed to exist as an exposed "tail" responsible for binding to progelatinase A and for increasing the rate of inhibition of active gelatinase A through electrostatic interactions with the C-terminal domain of the enzyme. The C-terminal domains of both TIMP-1 and TIMP-2 participate in low-affinity interactions with the C-terminal domain of gelatinase A which increase the rate of association by a factor of about 100 in both cases.
The work concentrates on a kinetic analysis of factors affecting the rate of association of the inhibitors with gelatinase A and demonstrates that the C-terminal domains of both proteins play an important role in controlling the rate of reaction with active enzyme. C-Terminal domain interactions are also responsible for the binding of TIMP-2 to progelatinase A.
The C-terminal nine amino acid peptide of TIMP-2 appears to make an important contribution to the rate of reaction because when this is removed the rate constant decreases approximately 4-fold to resemble that of TIMP-1. The marked decrease in the rate of inhibition by TIMP-2 with increasing ionic strength confirms the importance of ionic interactions to its mechanism. The effect is considerably decreased with the forms of TIMP-2 that lack the C-terminal peptide and is insignificant in the case of TIMP-1. Thus, the C-terminus of TIMP-2 is primarily, although not completely, responsible for the ionic interactions with gelatinase A.
Protein: DP03256 (UniProt P08253)
Region: residues 450	to 460
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
No electron density was observed for the NH2-terminal residue Ala30 and for residues Ser448 to Leu461 of the hinge region.
Cross-references: PDB:1CK7
Protein: DP03256 (UniProt P08253)
Region: residues 450	to 460
Annotation: flexible linker (Disorder function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
No electron density was observed for the NH2-terminal residue Ala30 and for residues Ser448 to Leu461 of the hinge region.
The COOH-terminal hemopexin-like domain of MMPs is linked to the catalytic domain by a hinge peptide, and it may determine the substrate specificity of MMPs.
Cross-references: PDB:1CK7
Protein: DP03257 (UniProt P03956)
Region: residues 20	to 31
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
In the structure described here, the first 12 residues of the prodomain (Phe1-Val12) are not visible in the electron density and are probably flexible.
Cross-references: PDB:1SU3
Protein: DP03257 (UniProt P03956)
Region: residues 46	to 57
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Except for the prodomain residues 27–38 and 80–87 the main chains can be traced in continuous electron density.
Twelve residues (Asn27-Ser38) of loop 1 are not visible in the electron density, suggesting that this region is flexible in solution. The flexible part of loop 1 contains the EKRRN sequence of the “bait” region. This EKRRN peptide would be positioned distal to the catalytic domain and is expected to be fully exposed to the solvent, which would provide maximum accessibility for activating proteases such as plasmin, plasma kallikrein, and trypsin (29).
The residues of loop 1 that contain the proteinase susceptible “bait” region are missing and therefore presumed flexible.
The IDR described here and not visible in DPB:1SU3 corresponds to residues 46-57 of the corresponding UniProt sequence.
Cross-references: PDB:1SU3
Protein: DP03257 (UniProt P03956)
Region: residues 52	to 56
Annotation: limited proteolysis display site (Disorder function)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
Since the Thr64-Leu65 bond is unlikely to be cleaved by these serine proteinases, we postulated that these enzymes initially cleave peptide bonds closer to the NH2 terminus in the propeptide to produce initial intermediates which, in turn, cleave the Thr64-Leu65 bond. To confirm this, procollagenase was incubated with plasma kallikrein (2 ug/mL) or plasmin (10 ug/mL) at 0C for 16 h to minimize the proteolytic action of collagenase intermediates. SDS/PAGE analyses of these products showed intermediates with Mr = 46000 (Figure 8). Sequence analysis of the intermediate generated by plasma kallikrein demonstrated that the Arg35-Arg36 and Arg36-Asn37 bonds were initially attacked by this enzyme. The results agree with the specificity of plasma kallikrein. It is therefore concluded that the formation of the 43 000-Mr species by serine proteinases is a two-step process (Figure 9B).
Asn37 corresponds to Asn56 of the EKRRN sequence in UniProt numbering
Protein: DP03258 (UniProt Q60841)
Region: residues 1222	to 1293
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The crystals have one R3 molecule per asymmetric unit, and 301 out of 387 residues of the R3 construct are visible in the electron density (Figure 2).
As the quality of the electron density corresponding to the N-terminal (1222–1293) and a loop (1393–1398) segment was poor, we omitted these segments from the final model.
Cross-references: PDB:2DDU
Protein: DP03259 (UniProt P13674)
Region: residues 151	to 160
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The return helix α4 is further connected to the PSB domain via a linker region (residues 104–143), forming two helices (α5 and α6) and an extended loop region (Figure 3).
The dimerization interactions within the four-helix bundle (between helices α1, α3, and α4), are complemented by interactions of the linker region. This region consists of two α helices, α5 and α6, and a loop following α6 (Figure 4B). This loop (residues 135–144) is either disordered, or modeled with high B factors (average B factor ranging from 35 to 122 Å2), indicating high flexibility (see Figure S2).
Cross-references: PDB:4BT8
Protein: DP03260 (UniProt O60568)
Region: residues 72	to 86
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Among these, a very flexible surface loop comprising residues Gly72 to Gly87 is not visible in the electron density of ligand-free LH3 structures. This loop contains several residues highly conserved among LH isoforms (Supplementary Fig. 9), which are not found in other glycosyltransferases.
Cross-references: PDB:6FXK
Protein: DP03260 (UniProt O60568)
Region: residues 592	to 605
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Residues 590–610 constitute a flexible loop capping the LH catalytic site.
Cross-references: PDB:6FXK
Protein: DP03260 (UniProt O60568)
Region: residues 73	to 77
Annotation: molecular function regulator (Molecular function)
Evidence: mutant phenotype evidence used in manual assertion
Supporting statements:
Structurally related glycosyltransferases also often bear tyrosine residues stacking with the UDP moiety, but these residues are located far in sequence from the canonical DxD motif40,41 responsible for metal ion coordination. Site-directed mutagenesis on Trp75 or Tyr114 into alanine residues yielded folded, but almost completely inactive LH3 variants (Fig. 2c, Supplementary fig. 11). Binding data using SPR on synthetic collagen peptides showed very limited differences between wild-type and mutant LH3 (Supplementary Fig. 11D). Together, these results highlight the distinguishing roles of Trp75 and Tyr114 in donor substrate binding and stabilization.
Trp75 stabilizes the UDP binding
Protein: DP03260 (UniProt O60568)
Region: residues 72	to 86
Annotation: disorder to order (Structural transition)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
Nonetheless, binding of these donor substrates induced dramatic conformational changes in the enzyme’s catalytic site, with full stabilization of the flexible Gly72-Gly87 loop in a “closed” conformation (Fig. 2b). The UDP pyrophosphate group is stabilized by interactions with Mn2+ and hydrogen bonding with Lys259 and backbone nitrogen of Gly256; both residues are positioned in a uniquely shaped α-helix located at the C-terminus of the domain.
Flexible loop 72–87 becomes well defined only in donor substrate-bound structures
The uracil moiety is sandwiched through π-π stacking interactions between Trp75 and Tyr114, and is stabilized by hydrogen bonding with Thr46 (Fig. 2a, b, Supplementary Fig. 10). Of note, these two residues highlight an unprecedented arrangement of UDP binding residues in glycosyltransferases: Trp75 belongs to the distinctive LH3 flexible loop covering residues Gly72-Gly87, that becomes fully stabilized upon substrate binding (Fig. 2b); Tyr114 is part of a non-canonical DxxD motif (Supplementary fig. 9), where Asp112, and Asp115 are responsible for Mn2+ coordination.
Cross-references: PDB:6FXT
PDB:6FXR
PDB:6FXY
PDB:6FXX
Protein: DP03260 (UniProt O60568)
Region: residues 73	to 77
Annotation: small molecule binding (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
Nonetheless, binding of these donor substrates induced dramatic conformational changes in the enzyme’s catalytic site, with full stabilization of the flexible Gly72-Gly87 loop in a “closed” conformation (Fig. 2b). The UDP pyrophosphate group is stabilized by interactions with Mn2+ and hydrogen bonding with Lys259 and backbone nitrogen of Gly256; both residues are positioned in a uniquely shaped α-helix located at the C-terminus of the domain.
Flexible loop 72–87 becomes well defined only in donor substrate-bound structures
The uracil moiety is sandwiched through π-π stacking interactions between Trp75 and Tyr114, and is stabilized by hydrogen bonding with Thr46 (Fig. 2a, b, Supplementary Fig. 10). Of note, these two residues highlight an unprecedented arrangement of UDP binding residues in glycosyltransferases: Trp75 belongs to the distinctive LH3 flexible loop covering residues Gly72-Gly87, that becomes fully stabilized upon substrate binding (Fig. 2b); Tyr114 is part of a non-canonical DxxD motif (Supplementary fig. 9), where Asp112, and Asp115 are responsible for Mn2+ coordination.
Residues involved in coordination of the metal ion are shown with orange sticks, while residues interacting and stabilizing UDP binding are shown in blue.
Nearly all residues surrounding the UDP moiety and shaping the LH3 glycosyltransferase catalytic site are conserved, including those involved in the unprecedented mode of UDP-substrate stabilization characterized by dual π-π stacking with Trp75 and Tyr114.
Trp75 stabilizes the UDP binding.
Cross-references: PDB:6FXT
PDB:6FXR
PDB:6FXY
PDB:6FXX
Protein: DP03260 (UniProt O60568)
Region: residues 73	to 77
Annotation: molecular function regulator (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
Nonetheless, binding of these donor substrates induced dramatic conformational changes in the enzyme’s catalytic site, with full stabilization of the flexible Gly72-Gly87 loop in a “closed” conformation (Fig. 2b). The UDP pyrophosphate group is stabilized by interactions with Mn2+ and hydrogen bonding with Lys259 and backbone nitrogen of Gly256; both residues are positioned in a uniquely shaped α-helix located at the C-terminus of the domain.
Flexible loop 72–87 becomes well defined only in donor substrate-bound structures
The uracil moiety is sandwiched through π-π stacking interactions between Trp75 and Tyr114, and is stabilized by hydrogen bonding with Thr46 (Fig. 2a, b, Supplementary Fig. 10). Of note, these two residues highlight an unprecedented arrangement of UDP binding residues in glycosyltransferases: Trp75 belongs to the distinctive LH3 flexible loop covering residues Gly72-Gly87, that becomes fully stabilized upon substrate binding (Fig. 2b); Tyr114 is part of a non-canonical DxxD motif (Supplementary fig. 9), where Asp112, and Asp115 are responsible for Mn2+ coordination.
Residues involved in coordination of the metal ion are shown with orange sticks, while residues interacting and stabilizing UDP binding are shown in blue.
Nearly all residues surrounding the UDP moiety and shaping the LH3 glycosyltransferase catalytic site are conserved, including those involved in the unprecedented mode of UDP-substrate stabilization characterized by dual π-π stacking with Trp75 and Tyr114.
Trp75 stabilizes the UDP binding.
Protein: DP03260 (UniProt O60568)
Region: residues 593	to 597
Annotation: metal ion binding (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
Analysis of electron density maps allowed the identification of a second Fe2+ in the LH domain, coordinated by residues His595, Asp597, Asp611 and His613 (Fig. 3b). Metal ion coordination stabilizes the flexible capping loop 590–610 into a conformation that completely plugs the LH catalytic site, in proximity to the dimer interface (Supplementary Fig. 16A). We could observe a very similar arrangement, although slightly more flexible, by replacing Fe2+ with Mn2+ in crystallization experiments (Supplementary Fig. 16B).
Co-crystallizations with Fe2+ allow identification of a second metal ion bound near the LH catalytic site that stabilizes the flexible capping loop 590–610 (shown in pink)
Four residues coordinate the binding of the second Fe2+ in metal ion-inhibited structures: His595, Asp597, Asp611 and His613. Two of them, His595 and His597, are localized in the flexible capping loop of the protein. This annotation describes His595.
Protein: DP03260 (UniProt O60568)
Region: residues 593	to 597
Annotation: iron ion binding (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
Co-crystallizations with Fe2+ allow identification of a second metal ion bound near the LH catalytic site that stabilizes the flexible capping loop 590–610 (shown in pink).
Analysis of electron density maps allowed the identification of a second Fe2+ in the LH domain, coordinated by residues His595, Asp597, Asp611 and His613 (Fig. 3b). Metal ion coordination stabilizes the flexible capping loop 590–610 into a conformation that completely plugs the LH catalytic site, in proximity to the dimer interface (Supplementary Fig. 16A). We could observe a very similar arrangement, although slightly more flexible, by replacing Fe2+ with Mn2+ in crystallization experiments (Supplementary Fig. 16B).
Four residues coordinate the Fe2+ binding: His595, Asp597, Asp611 and His613. Two of them, His595 and His597, are localized in the flexible capping loop of the protein. This annotation describes His595.
Protein: DP03260 (UniProt O60568)
Region: residues 595	to 599
Annotation: iron ion binding (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
Co-crystallizations with Fe2+ allow identification of a second metal ion bound near the LH catalytic site that stabilizes the flexible capping loop 590–610 (shown in pink).
Analysis of electron density maps allowed the identification of a second Fe2+ in the LH domain, coordinated by residues His595, Asp597, Asp611 and His613 (Fig. 3b). Metal ion coordination stabilizes the flexible capping loop 590–610 into a conformation that completely plugs the LH catalytic site, in proximity to the dimer interface (Supplementary Fig. 16A). We could observe a very similar arrangement, although slightly more flexible, by replacing Fe2+ with Mn2+ in crystallization experiments (Supplementary Fig. 16B).
Four residues coordinate the Fe2+ binding: His595, Asp597, Asp611 and His613. Two of them, His595 and Asp597, are localized in the flexible capping loop of the protein. This annotation describes Asp597.
Protein: DP03260 (UniProt O60568)
Region: residues 595	to 599
Annotation: metal ion binding (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
Co-crystallizations with Fe2+ allow identification of a second metal ion bound near the LH catalytic site that stabilizes the flexible capping loop 590–610 (shown in pink).
Analysis of electron density maps allowed the identification of a second Fe2+ in the LH domain, coordinated by residues His595, Asp597, Asp611 and His613 (Fig. 3b). Metal ion coordination stabilizes the flexible capping loop 590–610 into a conformation that completely plugs the LH catalytic site, in proximity to the dimer interface (Supplementary Fig. 16A). We could observe a very similar arrangement, although slightly more flexible, by replacing Fe2+ with Mn2+ in crystallization experiments (Supplementary Fig. 16B).
Four residues coordinate the binding of the second Fe2+ in metal ion-inhibited structures: His595, Asp597, Asp611 and His613. Two of them, His595 and His597, are localized in the flexible capping loop of the protein. This annotation describes Asp597.