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Title :   FIRST STRUCTURE OF A SNAKE VENOM METALLOPROTEINASE: A PROTOTYPE FOR MATRIX METALLOPROTEINASES(SLASH)COLLAGENASES

Authors :   F. -X. Gomis-Rueth, W. Bode

Date :   09 May 94 (Deposition) - 31 Aug 94 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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

Keywords :   Metalloprotease (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   F. X. Gomis-Ruth, L. F. Kress, W. Bode
First Structure Of A Snake Venom Metalloproteinase: A Prototype For Matrix Metalloproteinases/Collagenases.
Embo J. V. 12 4151 1993
PubMed-ID: 8223430
(for further references see the PDB file header)

Molecule 1 - ADAMALYSIN II
	Chains	:	A
	EC Number	:	3.4.24.46
	Engineered	:	YES
	Organism Common	:	EASTERN DIAMONDBACK RATTLESNAKE
	Organism Scientific	:	CROTALUS ADAMANTEUS
	Organism Taxid	:	8729

		1
Asymmetric Unit	:	A
Biological Unit 1 (2x)	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 3)

No.	Name	Count	Type	Full Name
1	CA	1	Ligand/Ion	CALCIUM ION
2	SO4	1	Ligand/Ion	SULFATE ION
3	ZN	1	Ligand/Ion	ZINC ION

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	SO4	2	Ligand/Ion	SULFATE ION
3	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:142 , HIS A:146 , HIS A:152 , HOH A:300	BINDING SITE FOR RESIDUE ZN A 999
2	AC2	SOFTWARE	GLU A:9 , ASP A:93 , GLN A:196 , CYS A:197 , ASN A:200 , HOH A:313	BINDING SITE FOR RESIDUE CA A 250
3	AC3	SOFTWARE	PRO A:4 , ARG A:6	BINDING SITE FOR RESIDUE SO4 A 260

Asymmetric Unit

No.	Residues
1	A:117	-	A:197
2	A:157	-	A:164

(no "Cis Peptide Bond" information available for 1IAG)

(no "SAP(SNP)/Variant" information available for 1IAG)

Asymmetric Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ADAM_MEPRO	PS50215	ADAM type metalloprotease domain profile.	VM12_CROAD	7-203	1	A:6-202
2	ZINC_PROTEASE	PS00142	Neutral zinc metallopeptidases, zinc-binding region signature.	VM12_CROAD	140-149	1	A:139-148

Biological Unit 1 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ADAM_MEPRO	PS50215	ADAM type metalloprotease domain profile.	VM12_CROAD	7-203	2	A:6-202
2	ZINC_PROTEASE	PS00142	Neutral zinc metallopeptidases, zinc-binding region signature.	VM12_CROAD	140-149	2	A:139-148

(no "Exon" information available for 1IAG)

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
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Chain A from PDB  Type:PROTEIN  Length:201
 aligned with VM12_CROAD | P34179 from UniProtKB/Swiss-Prot  Length:203

    Alignment length:201
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202 
           VM12_CROAD     3 NLPQRYIELVVVADRRVFMKYNSDLNIIRTRVHEIVNIINGFYRSLNIDVSLVNLEIWSGQDPLTIQSSSSNTLNSEGLWREKVLLNKKKKDNAQLLTAIEFKCETLGKAYLNSMCNPRSSVGIVKDHSPINLLVAVTMAHELGHNLGMEHDGKDCLRGASLCIMRPGLTPGRSYEFSDDSMGYYQKFLNQYKPQCILNKP 203
               SCOP domains d1iaga_ A: Snake venom metalloprotease                                                                                                                                                                    SCOP domains
               CATH domains 1iagA00 A:2-202 Collagenase (Catalytic Domain)                                                                                                                                                            CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
     Sec.struct. author (1) ....eeeeeeeeehhhhhhhh..hhhhhhhhhhhhhhhhhhhhh..eeeeeeeeeeee..........hhhhhhhhhhhhhhhhhhhhhhhhhhhh--........eeeee.........eeeeeee...hhhhhhhhhhhhhhhhhh.............................hhhhhhhhhhhhhhhh........ Sec.struct. author (1)
     Sec.struct. author (2) -------------------------------------------------------------------------------------------eeeeeee------------------------------------------------------------------------------------------------------- Sec.struct. author (2)
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----ADAM_MEPRO  PDB: A:6-202 UniProt: 7-203                                                                                                                                                               PROSITE (1)
                PROSITE (2) -----------------------------------------------------------------------------------------------------------------------------------------ZINC_PROTE------------------------------------------------------ PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1iag A   2 NLPQRYIELVVVADRRVFMKYNSDLNIIRTRVHEIVNIINKFYRSLNIRVSLTDLEIWSGQDFITIQSSSSNTLNSFGEWRERVLLIWKRHDNAQLLTAINFEGKIIGKAYTSSMCNPRSSVGIVKDHSPINLLVAVTMAHELGHNLGMEHDGKDCLRGASLCIMRPGLTPGRSYEFSDDSMGYYQKFLNQYKPQCILNKP 202
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201

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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: Zincin-like (701)

Superfamily: Metalloproteases (zincins), catalytic domain (647)

Family: Reprolysin-like (24)

Protein domain: Snake venom metalloprotease (20)

Eastern diamondback rattlesnake (Crotalus adamanteus), adamalysin II [TaxId: 8729] (4)

d1iaga_

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Collagenase (Catalytic Domain) (236)

Homologous Superfamily: Collagenase (Catalytic Domain) (234)

Eastern diamondback rattlesnake (Crotalus adamanteus) (4)

1iagA00

A:2-202

(no "Pfam Domain" information available for 1IAG)

Asymmetric Unit(hide GO term definitions)

Chain A (VM12_CROAD | P34179)

molecular function
	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.
biological process
	GO:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
cellular component
	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.

Asymmetric Unit
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Biological Unit
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	VM12_CROAD \| P34179	:	2aig 3aig 4aig

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