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Title :   CRYSTAL STRUCTURE OF THE COMPLEX BETWEEN MMP-8 AND A NON-ZINC CHELATING INHIBITOR

Authors :   G. Pochetti, R. Montanari, F. Mazza

Date :   02 Jul 08 (Deposition) - 03 Mar 09 (Release) - 03 Mar 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)

Keywords :   Hydrolase, Selective Inhibition, Non-Zinc Chelating Inhibitors, Calcium, Collagen Degradation, Extracellular Matrix, Glycoprotein, Metal-Binding, Metalloprotease, Polymorphism, Protease, Secreted, Zinc, Zymogen (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   G. Pochetti, R. Montanari, C. Gege, C. Chevrier, A. G. Taveras, F. Mazza
Extra Binding Region Induced By Non-Zinc Chelating Inhibitors Into The S(1)' Subsite Of Matrix Metalloproteinase 8 (Mmp-8)
J. Med. Chem. V. 52 1040 2009
PubMed-ID: 19173605 | Reference-DOI: 10.1021/JM801166J
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 10)

Sites (10, 10)

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASP A:137 , GLY A:169 , GLY A:171 , ASP A:173	BINDING SITE FOR RESIDUE CA A 996
02	AC2	SOFTWARE	ASP A:154 , GLY A:155 , ASN A:157 , ILE A:159 , ASP A:177 , GLU A:180	BINDING SITE FOR RESIDUE CA A 997
03	AC3	SOFTWARE	HIS A:147 , ASP A:149 , HIS A:162 , HIS A:175	BINDING SITE FOR RESIDUE ZN A 998
04	AC4	SOFTWARE	HIS A:197 , HIS A:201 , HIS A:207	BINDING SITE FOR RESIDUE ZN A 999
05	AC5	SOFTWARE	ASP B:137 , GLY B:169 , GLY B:171 , ASP B:173	BINDING SITE FOR RESIDUE CA B 996
06	AC6	SOFTWARE	ASP B:154 , GLY B:155 , ASN B:157 , ILE B:159 , ASP B:177 , GLU B:180	BINDING SITE FOR RESIDUE CA B 997
07	AC7	SOFTWARE	HIS B:147 , ASP B:149 , HIS B:162 , HIS B:175	BINDING SITE FOR RESIDUE ZN B 998
08	AC8	SOFTWARE	HIS B:197 , HIS B:201 , HIS B:207	BINDING SITE FOR RESIDUE ZN B 999
09	AC9	SOFTWARE	PHE A:192 , LEU A:193 , HIS A:197 , ALA A:213 , LEU A:214 , TYR A:216 , PRO A:217 , ASN A:218 , TYR A:219 , ALA A:220 , PHE A:221 , ARG A:222 , THR A:224 , TYR A:227 , SER A:228	BINDING SITE FOR RESIDUE AXA A 1
10	BC1	SOFTWARE	LEU B:193 , HIS B:197 , ALA B:213 , LEU B:214 , TYR B:216 , PRO B:217 , ASN B:218 , TYR B:219 , ALA B:220 , PHE B:221 , ARG B:222 , THR B:224 , TYR B:227 , SER B:228	BINDING SITE FOR RESIDUE AXA B 2

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (3, 6)

Asymmetric Unit (3, 6)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_025038	G	154	E	MMP8_HUMAN	Polymorphism	35056226	A/B	G	134	E
2	UniProt	VAR_025039	D	193	V	MMP8_HUMAN	Polymorphism	34428739	A/B	D	173	V
3	UniProt	VAR_025040	N	246	Y	MMP8_HUMAN	Polymorphism	35243553	A/B	N	226	Y

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 1 (3, 3)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_025038	G	154	E	MMP8_HUMAN	Polymorphism	35056226	A	G	134	E
2	UniProt	VAR_025039	D	193	V	MMP8_HUMAN	Polymorphism	34428739	A	D	173	V
3	UniProt	VAR_025040	N	246	Y	MMP8_HUMAN	Polymorphism	35243553	A	N	226	Y

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 2 (3, 3)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_025038	G	154	E	MMP8_HUMAN	Polymorphism	35056226	B	G	134	E
2	UniProt	VAR_025039	D	193	V	MMP8_HUMAN	Polymorphism	34428739	B	D	173	V
3	UniProt	VAR_025040	N	246	Y	MMP8_HUMAN	Polymorphism	35243553	B	N	226	Y

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

PROSITE Motifs (1, 2)

Exons (5, 10)

Asymmetric Unit (5, 10)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.2b	ENST00000236826	2b	ENSE00002164267	chr11:102595685-102595485	201	MMP8_HUMAN	1-34	34	0	-	-
1.6c	ENST00000236826	6c	ENSE00001770190	chr11:102593404-102593160	245	MMP8_HUMAN	35-116	82	2	A:80-96 B:80-96	17 17
1.7	ENST00000236826	7	ENSE00000795297	chr11:102592493-102592345	149	MMP8_HUMAN	116-166	51	2	A:96-146 B:96-146	51 51
1.8b	ENST00000236826	8b	ENSE00000795296	chr11:102592257-102592132	126	MMP8_HUMAN	166-208	43	2	A:146-188 B:146-188	43 43
1.9	ENST00000236826	9	ENSE00001105479	chr11:102589306-102589145	162	MMP8_HUMAN	208-262	55	2	A:188-242 B:188-242	55 55
1.10	ENST00000236826	10	ENSE00001105482	chr11:102587150-102587033	118	MMP8_HUMAN	262-301	40	2	A:242-242 B:242-242	1 1
1.11	ENST00000236826	11	ENSE00001105475	chr11:102586168-102586035	134	MMP8_HUMAN	301-346	46	0	-	-
1.12	ENST00000236826	12	ENSE00001105489	chr11:102585440-102585287	154	MMP8_HUMAN	346-397	52	0	-	-
1.13	ENST00000236826	13	ENSE00001105495	chr11:102584588-102584485	104	MMP8_HUMAN	397-432	36	0	-	-
1.14c	ENST00000236826	14c	ENSE00001322445	chr11:102584188-102582526	1663	MMP8_HUMAN	432-467	36	0	-	-

Sequences/Alignments

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:163
 aligned with MMP8_HUMAN | P22894 from UniProtKB/Swiss-Prot  Length:467

    Alignment length:163
                                   109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259   
           MMP8_HUMAN   100 MLTPGNPKWERTNLTYRIRNYTPQLSEAEVERAIKDAFELWSVASPLIFTRISQGEADINIAFYQRDHGDNSPFDGPNGILAHAFQPGQGIGGDAHFDAEETWTNTSANYNLFLVAAHEFGHSLGLAHSSDPGALMYPNYAFRETSNYSLPQDDIDGIQAIYG 262
               SCOP domains d3dnga_ A: Neutrophil collagenase (MMP-8)                                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeeeee.......hhhhhhhhhhhhhhhhhh....eeee.......eeeeee.................eee..........eeee............hhhhhhhhhhhhhhh.........................hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------E--------------------------------------V----------------------------------------------------Y---------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------ZINC_PROTE--------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.6c        -------------------------------------------------Exon 1.8b  PDB: A:146-188 UniProt: 166-208 -----------------------------------------------------1 Transcript 1 (1)
           Transcript 1 (2) ----------------Exon 1.7  PDB: A:96-146 UniProt: 116-166           -----------------------------------------Exon 1.9  PDB: A:188-242 UniProt: 208-262               Transcript 1 (2)
                 3dng A  80 MLTPGNPKWERTNLTYRIRNYTPQLSEAEVERAIKDAFELWSVASPLIFTRISQGEADINIAFYQRDHGDNSPFDGPNGILAHAFQPGQGIGGDAHFDAEETWTNTSANYNLFLVAAHEFGHSLGLAHSSDPGALMYPNYAFRETSNYSLPQDDIDGIQAIYG 242
                                    89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239

Chain B from PDB  Type:PROTEIN  Length:163
 aligned with MMP8_HUMAN | P22894 from UniProtKB/Swiss-Prot  Length:467

    Alignment length:163
                                   109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259   
           MMP8_HUMAN   100 MLTPGNPKWERTNLTYRIRNYTPQLSEAEVERAIKDAFELWSVASPLIFTRISQGEADINIAFYQRDHGDNSPFDGPNGILAHAFQPGQGIGGDAHFDAEETWTNTSANYNLFLVAAHEFGHSLGLAHSSDPGALMYPNYAFRETSNYSLPQDDIDGIQAIYG 262
               SCOP domains d3dngb_ B: Neutrophil collagenase (MMP-8)                                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeeeee.......hhhhhhhhhhhhhhhhhh....eeee.......eeeeee.................eee..........eeee............hhhhhhhhhhhhhh..........................hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------E--------------------------------------V----------------------------------------------------Y---------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------ZINC_PROTE--------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.6c        -------------------------------------------------Exon 1.8b  PDB: B:146-188 UniProt: 166-208 -----------------------------------------------------1 Transcript 1 (1)
           Transcript 1 (2) ----------------Exon 1.7  PDB: B:96-146 UniProt: 116-166           -----------------------------------------Exon 1.9  PDB: B:188-242 UniProt: 208-262               Transcript 1 (2)
                 3dng B  80 MLTPGNPKWERTNLTYRIRNYTPQLSEAEVERAIKDAFELWSVASPLIFTRISQGEADINIAFYQRDHGDNSPFDGPNGILAHAFQPGQGIGGDAHFDAEETWTNTSANYNLFLVAAHEFGHSLGLAHSSDPGALMYPNYAFRETSNYSLPQDDIDGIQAIYG 242
                                    89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (16, 16)

Asymmetric Unit(hide GO term definitions)

Chain A,B (MMP8_HUMAN | P22894)

molecular function
	GO:0005509	calcium ion binding	Interacting selectively and non-covalently with calcium ions (Ca2+).
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0004222	metalloendopeptidase activity	Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions.
	GO:0008237	metallopeptidase activity	Catalysis of the hydrolysis of peptide bonds by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions.
	GO:0008233	peptidase activity	Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
	GO:0004252	serine-type endopeptidase activity	Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0030574	collagen catabolic process	The proteolytic chemical reactions and pathways resulting in the breakdown of collagen in the extracellular matrix, usually carried out by proteases secreted by nearby cells.
	GO:0035987	endodermal cell differentiation	The process in which a relatively unspecialized cell acquires the specialized features of an endoderm cell, a cell of the inner of the three germ layers of the embryo.
	GO:0022617	extracellular matrix disassembly	A process that results in the breakdown of the extracellular matrix.
	GO:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
cellular component
	GO:0031012	extracellular matrix	A structure lying external to one or more cells, which provides structural support for cells or tissues.
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
	GO:0005615	extracellular space	That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
	GO:0005578	proteinaceous extracellular matrix	A layer consisting mainly of proteins (especially collagen) and glycosaminoglycans (mostly as proteoglycans) that forms a sheet underlying or overlying cells such as endothelial and epithelial cells. The proteins are secreted by cells in the vicinity. An example of this component is found in Mus musculus.

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