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(-) Description

Title :  CRYSTAL STRUCTURE OF A PUTATIVE MODULATOR OF DNA GYRASE (BT3649) FROM BACTEROIDES THETAIOTAOMICRON VPI-5482 AT 1.75 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  15 Oct 04  (Deposition) - 09 Nov 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Putative Modulator Of Dna Gyrase, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Putative Modulator Of Dna Gyrase (Bt3649) From Bacteroides Thetaiotaomicron Vpi-5482 At 1. 75 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PUTATIVE MODULATOR OF DNA GYRASE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: BT3649
    Organism Scientific: BACTEROIDES THETAIOTAOMICRON
    Organism Taxid: 226186
    Strain: VPI-5482

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1EDO4Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:292 , GLY A:293 , ALA A:294 , HOH A:604BINDING SITE FOR RESIDUE EDO A 440
2AC2SOFTWARELYS A:274 , SER A:277 , ASP A:278 , LEU A:411 , HOH A:483 , HOH A:618 , HOH A:731BINDING SITE FOR RESIDUE EDO A 441

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1VPB)

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1VPB)

(-) Exons   (0, 0)

(no "Exon" information available for 1VPB)

(-) 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:437
 aligned with Q8A1L2_BACTN | Q8A1L2 from UniProtKB/TrEMBL  Length:439

    Alignment length:439
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430         
         Q8A1L2_BACTN     1 MITDENKKLAQWAMDYALKNGCQAAKVLLYSSSNTSFELRDAKMDRLQQASEGGLSLSLYVDGRYGSISTNRLNRKELETFIKNGIDSTRYLAKDEARVLADPSRYYKGGKPDLKLYDAKFASLNPDDKIEMAKAVAEEALGKDERIISVGSSYGDGEDFAYRLISNGFEGETKSTWYSLSADITIRGEGEARPSAYWYESSLYMNDLIKKGIGQKALERVLRKLGQKKVQSGKYTMVVDPMNSSRLLSPMISALNGSALQQKNSFLLNKLNEKIASDRLTLTDEPHLVKASGARYFDNEGIATERRSIFDKGVLNTYFIDTYNAKKMGVDPTISGSSILVMETGDKNLDGLIAGVEKGILVTGFNGGNNNSSTGDFSYGIEGFLIENGKLTQPVSEMNVTGNLITLWNSLVATGNDPRLNSSWRIPSLVFEGVDFSGL 439
               SCOP domains d1vpba_ A: Putative modulator of DNA gyra  se BT3649                                                                                                                                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------PmbA_TldD-1vpbA01 A  :23-318                                                                                                                                                                                                                                                                            ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhh...eeeeeeeeeeeeeeeee.--..eeeeeeeeeeeeeeee..eeeeeee...hhhhhhhhhhhhhhhhh...........hhhhh.............hhhhhhhhhhhhhhhhhhhh.......eeeeeeeeeeeeeeeeeee...eeeeeeeeeeeeeeeeee........eeeeeeee.hhhhh...hhhhhhhhhhhh.........eeeeeee...hhhhhhhhhhhh.hhhhhhh...................eee......................eeeee..ee.....hhhhhhhhh..........eee.....hhhhhhhh..eeeeeeeeeeeee.....eeeeeeeeeeee..eeeeeeeeeeeeeehhhhhhheeee.........ee...eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vpb A   1 MITDENKKLAQWAMDYALKNGCQAAKVLLYSSSNTSFELRD--MDRLQQASEGGLSLSLYVDGRYGSISTNRLNRKELETFIKNGIDSTRYLAKDEARVLADPSRYYKGGKPDLKLYDAKFASLNPDDKIEMAKAVAEEALGKDERIISVGSSYGDGEDFAYRLISNGFEGETKSTWYSLSADITIRGEGEARPSAYWYESSLYMNDLIKKGIGQKALERVLRKLGQKKVQSGKYTMVVDPMNSSRLLSPMISALNGSALQQKNSFLLNKLNEKIASDRLTLTDEPHLVKASGARYFDNEGIATERRSIFDKGVLNTYFIDTYNAKKMGVDPTISGSSILVMETGDKNLDGLIAGVEKGILVTGFNGGNNNSSTGDFSYGIEGFLIENGKLTQPVSEMNVTGNLITLWNSLVATGNDPRLNSSWRIPSLVFEGVDFSGL 439
                                    10        20        30        40|  |    50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430         
                                                                   41 44
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 Classification and Annotation

(-) SCOP Domains  (1, 1)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1VPB)

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: no clan defined [family: PmbA_TldD] (3)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q8A1L2_BACTN | Q8A1L2)
molecular function
    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.
biological process
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.

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