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(-) Description

Title :  CRYSTAL STRUCTURE OF A METALLO-ENDOPEPTIDASES (BACOVA_00663) FROM BACTEROIDES OVATUS AT 1.93 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  30 Sep 10  (Deposition) - 27 Oct 10  (Release) - 20 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.93
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-Biology, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of A Metallo-Endopeptidases (Bacova_00663 From Bacteroides Ovatus At 1. 93 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - METALLO-ENDOPEPTIDASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: SPEEDET
    Expression System Strain: HK100
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: SEQUENCE DATABASE RESIDUES 20-425
    Gene: BACOVA_00663
    Organism Scientific: BACTEROIDES OVATUS ATCC 8483
    Organism Taxid: 411476

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (7, 35)

Asymmetric/Biological Unit (7, 35)
No.NameCountTypeFull Name
1CL3Ligand/IonCHLORIDE ION
2DMS1Ligand/IonDIMETHYL SULFOXIDE
3K2Ligand/IonPOTASSIUM ION
4MSE17Mod. Amino AcidSELENOMETHIONINE
5PEG4Ligand/IonDI(HYDROXYETHYL)ETHER
6PO44Ligand/IonPHOSPHATE ION
7ZN4Ligand/IonZINC ION

(-) Sites  (18, 18)

Asymmetric Unit (18, 18)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:311 , HIS A:315 , ASP A:322 , PO4 A:433BINDING SITE FOR RESIDUE ZN A 426
02AC2SOFTWAREGLU A:323 , CYS A:398 , CYS A:409 , CYS A:412BINDING SITE FOR RESIDUE ZN A 427
03AC3SOFTWAREALA A:58 , GLU A:172 , CYS A:175 , ASP A:177 , GLU A:275 , HOH A:616BINDING SITE FOR RESIDUE K A 428
04AC4SOFTWARETHR A:227 , THR A:242 , ALA A:243BINDING SITE FOR RESIDUE CL A 430
05AC5SOFTWAREILE A:291 , TYR A:292 , HOH A:621 , HOH A:794 , HOH A:804BINDING SITE FOR RESIDUE CL A 431
06AC6SOFTWAREHIS A:311 , GLU A:312 , HIS A:315 , ASP A:322 , TYR A:324 , ASN A:328 , ZN A:426 , HOH A:854 , HOH A:926BINDING SITE FOR RESIDUE PO4 A 433
07AC7SOFTWAREGLN A:241 , HIS A:245 , HOH A:521 , HOH A:656 , HOH A:782 , HIS B:153 , ARG B:155 , HOH B:600BINDING SITE FOR RESIDUE PO4 A 434
08AC8SOFTWAREARG A:417 , ARG A:418 , GLU A:421 , HOH A:899BINDING SITE FOR RESIDUE PO4 A 436
09AC9SOFTWAREGLU A:70 , TYR A:131 , LYS A:135 , HOH A:588 , HOH A:1079BINDING SITE FOR RESIDUE DMS A 437
10BC1SOFTWAREGLN A:20 , HIS A:62 , HIS A:63 , GLU A:66 , HOH A:1035BINDING SITE FOR RESIDUE PEG A 438
11BC2SOFTWAREHIS B:311 , HIS B:315 , ASP B:322 , HOH B:546BINDING SITE FOR RESIDUE ZN B 426
12BC3SOFTWAREGLU B:323 , CYS B:398 , CYS B:409 , CYS B:412BINDING SITE FOR RESIDUE ZN B 427
13BC4SOFTWAREALA B:58 , GLU B:172 , CYS B:175 , ASP B:177 , GLU B:275 , HOH B:597BINDING SITE FOR RESIDUE K B 429
14BC5SOFTWARETYR B:292BINDING SITE FOR RESIDUE CL B 432
15BC6SOFTWARELYS B:78 , LYS B:83 , GLU B:125 , GLU B:127 , LYS B:142 , HOH B:841BINDING SITE FOR RESIDUE PO4 B 435
16BC7SOFTWAREGLN B:20 , HIS B:62 , HIS B:63 , GLU B:66 , HOH B:1023 , HOH B:1189BINDING SITE FOR RESIDUE PEG B 439
17BC8SOFTWAREGLU A:50 , HIS A:153 , ARG A:155 , GLN B:241 , HIS B:245 , ARG B:261BINDING SITE FOR RESIDUE PEG B 440
18BC9SOFTWAREARG B:199 , LYS B:306 , ARG B:349 , LYS B:357 , ILE B:366 , HOH B:929BINDING SITE FOR RESIDUE PEG B 441

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3P1V)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Glu A:208 -Pro A:209
2Ile A:366 -Pro A:367
3Glu B:208 -Pro B:209
4Ile B:366 -Pro B:367

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3P1V)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3P1V)

(-) Exons   (0, 0)

(no "Exon" information available for 3P1V)

(-) 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:406
 aligned with A7LS78_BACO1 | A7LS78 from UniProtKB/TrEMBL  Length:425

    Alignment length:406
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419      
         A7LS78_BACO1    20 QNFADYFQNKTLRVDYIFTGDATQQAIYLDELSQLPTWAGRQHHLSELPLEGNGQIIVKDLASKQCIYQTSFSSLFQEWLSTDEAKETAKGFENTFLLPYPKQPVEVEVTLYSPRKKTMATYKHIVRPDDILIHKRGVSHITPHRYMLQSGNEKDCIDVAILAEGYTEKEMDVFYQDAQRTCESLFSYEPFRSMKSKFNIVAVASPSTDSGVSVPRENQWKQTAVHSHFDTFYSDRYLTTSRVKSVHNALAGIPYEHIIILANTDVYGGGGIYNSYTLTTAHHPMFKPVVVHEFGHSFGGLADEYFYDNDVMTDTYPLDVEPWEQNISTRVNFASKWKDMLPSGAPIPTPIAEKKKYPVGVYEGGGYSAKGIYRPAYDCRMKTNEYPEFCPVCQRAIRRMIEFYVP 425
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhh.eeeeeeeeeeeeee....eeeeeeeeeee..................eeeeeee.....eeeeeee.hhhhhhhhhhhhhh..eeeeeeeeeeee...eeeeeeee.....eeeeeeeee.......ee........eeeeee.......eeeeeeee..hhhhhhhhhhhhhhhhhhhh.......hhh.eeeeee..........hhhhh...........hhhhh.......hhhhhhhhhh.....eeeeee......eeee...eeeee....hhhhhhhhhhhhhh.................................hhhhhhhhhh........hhhhh.......eeee..eeeeeee...............hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3p1v A  20 QNFADYFQNKTLRVDYIFTGDATQQAIYLDELSQLPTWAGRQHHLSELPLEGNGQIIVKDLASKQCIYQTSFSSLFQEWLSTDEAKETAKGFENTFLLPYPKQPVEVEVTLYSPRKKTmATYKHIVRPDDILIHKRGVSHITPHRYmLQSGNEKDCIDVAILAEGYTEKEmDVFYQDAQRTCESLFSYEPFRSmKSKFNIVAVASPSTDSGVSVPRENQWKQTAVHSHFDTFYSDRYLTTSRVKSVHNALAGIPYEHIIILANTDVYGGGGIYNSYTLTTAHHPmFKPVVVHEFGHSFGGLADEYFYDNDVmTDTYPLDVEPWEQNISTRVNFASKWKDmLPSGAPIPTPIAEKKKYPVGVYEGGGYSAKGIYRPAYDCRmKTNEYPEFCPVCQRAIRRmIEFYVP 425
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159      |169       179       189|      199       209   |   219       229       239       249       259       269       279       289       299    |  309       319       329 |     339       349       359       369       379       389       399|      409       419      
                                                                                                                                                138-MSE                     166-MSE                 190-MSE                213-MSE                                                                                    304-MSE                    331-MSE                     359-MSE                                  400-MSE            419-MSE  


Chain B from PDB  Type:PROTEIN  Length:404
 aligned with A7LS78_BACO1 | A7LS78 from UniProtKB/TrEMBL  Length:425

    Alignment length:407
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       
         A7LS78_BACO1    19 AQNFADYFQNKTLRVDYIFTGDATQQAIYLDELSQLPTWAGRQHHLSELPLEGNGQIIVKDLASKQCIYQTSFSSLFQEWLSTDEAKETAKGFENTFLLPYPKQPVEVEVTLYSPRKKTMATYKHIVRPDDILIHKRGVSHITPHRYMLQSGNEKDCIDVAILAEGYTEKEMDVFYQDAQRTCESLFSYEPFRSMKSKFNIVAVASPSTDSGVSVPRENQWKQTAVHSHFDTFYSDRYLTTSRVKSVHNALAGIPYEHIIILANTDVYGGGGIYNSYTLTTAHHPMFKPVVVHEFGHSFGGLADEYFYDNDVMTDTYPLDVEPWEQNISTRVNFASKWKDMLPSGAPIPTPIAEKKKYPVGVYEGGGYSAKGIYRPAYDCRMKTNEYPEFCPVCQRAIRRMIEFYVP 425
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhh.eeeeeeeeeeeeee....eeeeeeeeeee..................eeeeeee.....eeeeeee.hhhhhhhhhhhhhh..eeeeeeeeeeee...eeeeeeee.....eeeeeeeee.......ee........eeeeee.......eeeeeeee..hhhhhhhhhhhhhhhhhhhh.......hhh.eeeeee..........hhhhh...........hhhhh.......hhhhhhhhhh.....eeeeee......eeee...eeeee....hhhhhhhhhhhhhh.............---.................hhhhhhhhhh........hhhhh.......eeee..eeeeeee...............hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3p1v B   0 GQNFADYFQNKTLRVDYIFTGDATQQAIYLDELSQLPTWAGRQHHLSELPLEGNGQIIVKDLASKQCIYQTSFSSLFQEWLSTDEAKETAKGFENTFLLPYPKQPVEVEVTLYSPRKKTmATYKHIVRPDDILIHKRGVSHITPHRYmLQSGNEKDCIDVAILAEGYTEKEmDVFYQDAQRTCESLFSYEPFRSmKSKFNIVAVASPSTDSGVSVPRENQWKQTAVHSHFDTFYSDRYLTTSRVKSVHNALAGIPYEHIIILANTDVYGGGGIYNSYTLTTAHHPmFKPVVVHEFGHSFGGLADEYFYDNDV---TYPLDVEPWEQNISTRVNFASKWKDmLPSGAPIPTPIAEKKKYPVGVYEGGGYSAKGIYRPAYDCRmKTNEYPEFCPVCQRAIRRmIEFYVP 425
                            ||      28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188 |     198       208    |  218       228       238       248       258       268       278       288       298     | 308       318       328 |   | 338       348       358|      368       378       388       398 |     408       418|      
                            0|                                                                                                                   138-MSE                     166-MSE                 190-MSE                213-MSE                                                                                    304-MSE                   330 334                      359-MSE                                  400-MSE            419-MSE  
                            20
   Legend:   → Mismatch (orange background)
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 3P1V)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3P1V)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3P1V)

(-) Gene Ontology  (1, 1)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (A7LS78_BACO1 | A7LS78)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.

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