3TT4 - JenaLib

Title :   HUMAN MMP8 IN COMPLEX WITH L-GLUTAMATE MOTIF INHIBITOR

Authors :   E. A. Stura, V. Dive, L. Devel, B. Czarny, F. Beau, L. Vera

Date :   14 Sep 11 (Deposition) - 20 Jun 12 (Release) - 17 Oct 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.88

Chains :   Asym./Biol. Unit : A

Keywords :   Pseudo Dipeptides, Potent Inhibitors, Metzincin, Zinc Metalloprotease, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   L. Devel, F. Beau, M. Amoura, L. Vera, E. Cassar-Lajeunesse, S. Garcia B. Czarny, E. A. Stura, V. Dive
Simple Pseudo-Dipeptides With A P2' Glutamate: A Novel Inhibitor Family Of Matrix Metalloproteases And Other Metzincins.
J. Biol. Chem. V. 287 26647 2012
PubMed-ID: 22689580 | Reference-DOI: 10.1074/JBC.M112.380782

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 6)

Sites (6, 6)

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:147 , ASP A:149 , HIS A:162 , HIS A:175	BINDING SITE FOR RESIDUE ZN A 301
2	AC2	SOFTWARE	E1S A:1 , HIS A:197 , HIS A:201 , HIS A:207	BINDING SITE FOR RESIDUE ZN A 302
3	AC3	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 303
4	AC4	SOFTWARE	HOH A:33 , HOH A:34 , ASP A:137 , GLY A:169 , GLY A:171 , ASP A:173	BINDING SITE FOR RESIDUE CA A 304
5	AC5	SOFTWARE	HOH A:46 , THR A:129 , ARG A:130 , ILE A:159 , LEU A:160 , ALA A:161 , HIS A:197 , GLU A:198 , HIS A:201 , HIS A:207 , ALA A:213 , LEU A:214 , TYR A:216 , PRO A:217 , ASN A:218 , TYR A:219 , ALA A:220 , ARG A:222 , ZN A:302	BINDING SITE FOR RESIDUE E1S A 1
6	AC6	SOFTWARE	ALA A:112 , ASP A:115 , SER A:186 , PHE A:192 , THR A:224 , SER A:225 , ASN A:226 , HOH A:277	BINDING SITE FOR RESIDUE MES A 243

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (3, 3)

PROSITE Motifs (1, 1)

Exons (5, 5)

Asymmetric/Biological Unit (5, 5)

	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	1	A:84-96	13
1.7	ENST00000236826	7	ENSE00000795297	chr11:102592493-102592345	149	MMP8_HUMAN	116-166	51	1	A:96-146	51
1.8b	ENST00000236826	8b	ENSE00000795296	chr11:102592257-102592132	126	MMP8_HUMAN	166-208	43	1	A:146-188	43
1.9	ENST00000236826	9	ENSE00001105479	chr11:102589306-102589145	162	MMP8_HUMAN	208-262	55	1	A:188-242	55
1.10	ENST00000236826	10	ENSE00001105482	chr11:102587150-102587033	118	MMP8_HUMAN	262-301	40	1	A:242-242	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/Biological 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:159
 aligned with MMP8_HUMAN | P22894 from UniProtKB/Swiss-Prot  Length:467

    Alignment length:159
                                   113       123       133       143       153       163       173       183       193       203       213       223       233       243       253         
           MMP8_HUMAN   104 GNPKWERTNLTYRIRNYTPQLSEAEVERAIKDAFELWSVASPLIFTRISQGEADINIAFYQRDHGDNSPFDGPNGILAHAFQPGQGIGGDAHFDAEETWTNTSANYNLFLVAAHEFGHSLGLAHSSDPGALMYPNYAFRETSNYSLPQDDIDGIQAIYG 262
               SCOP domains d3tt4a_ A: automated matches                                                                                                                                    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: 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)
                 3tt4 A  84 GNPKWERTNLTYRIRNYTPQLSEAEVERAIKDAFELWSVASPLIFTRISQGEADINIAFYQRDHGDNSPFDGPNGILAHAFQPGQGIGGDAHFDAEETWTNTSANYNLFLVAAHEFGHSLGLAHSSDPGALMYPNYAFRETSNYSLPQDDIDGIQAIYG 242
                                    93       103       113       123       133       143       153       163       173       183       193       203       213       223       233

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, 1)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (16, 16)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (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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		Asn A:188 - Tyr A:189	[ RasMol ]

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