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(-) Description

Title :  CRYSTAL STRUCTURE OF A PUTATIVE MODULATOR OF A DNA GYRASE (TM0727) FROM THERMOTOGA MARITIMA MSB8 AT 1.95 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  09 Jul 04  (Deposition) - 21 Sep 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Pmba-Related Protein, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi, Gene Regulation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Rife, R. Schwarzenbacher, D. Mcmullan, P. Abdubek, E. Ambing, H. Axelrod, T. Biorac, J. M. Canaves, H. J. Chiu, A. M. Deacon, M. Didonato, M. A. Elsliger, A. Godzik, C. Grittini, S. K. Grzechnik, J. Hale, E. Hampton, G. W. Han, J. Haugen, M. Hornsby, L. Jaroszewski, H. E. Klock, E. Koesema, A. Kreusch, P. Kuhn, S. A. Lesley, M. D. Miller, K. Moy, E. Nigoghossian, J. Paulsen, K. Quijano, R. Reyes, E. Sims, G. Spraggon, R. C. Stevens, H. Van Den Bedem, J. Velasquez, J. Vincent, A. White, G. Wolf, Q. Xu, K. O. Hodgson, J. Wooley, I. A. Wilson
Crystal Structure Of A Putative Modulator Of Dna Gyrase (Pmba) From Thermotoga Maritima At 1. 95 A Resolution Reveal A New Fold.
Proteins V. 61 444 2005
PubMed-ID: 16104019  |  Reference-DOI: 10.1002/PROT.20468

(-) Compounds

Molecule 1 - PMBA-RELATED PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: TM0727
    Organism Scientific: THERMOTOGA MARITIMA
    Organism Taxid: 243274
    Strain: MSB8

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1VL4)

(-) Sites  (0, 0)

(no "Site" information available for 1VL4)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1VL4)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1VL4)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1VL4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1VL4)

(-) Exons   (0, 0)

(no "Exon" information available for 1VL4)

(-) 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:429
 aligned with Q9WZI6_THEMA | Q9WZI6 from UniProtKB/TrEMBL  Length:435

    Alignment length:433
                                    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   
         Q9WZI6_THEMA     1 MTFEEFKDRLFALAKKNGVEVQISFLETREFSLRLANGDLDQYTDAGKFNVEIKVLKDGKTGTFRTQVLENPEKCFEEALSNLQVKDSEEKEYFFEGGKEYREMETYVGRFEKLSVKEKMDMAKKAHESAAKDERVVMVPTVMYKDMVIKKIITNTLGLDVESQMDGGFLFAMAIARDANPRSGSWYELARTPEDLNPEEIGKRAAEEAISLIGSKTIPSGKYPVLMRNTALLDLMEMFIPMISAENVQKNLSPLKGKLGEQVGNPAVSIKDLPYHPKGLSSTPFDDEGVPTTEKFVLENGVLKTFLHNLKTARKEGVEPTGNGFVGGIRPVNLMLMPGEKSFEELLKEMDRGVVITEVEGMHAGANSISGEFSLFAKGYWVENGEIAHGVEDITISGNFLDLLRKIVLVGNDVKVSQHTIAPSVLVEVLDVA 433
               SCOP domains d1vl4a_ A: PmbA-related protein TM0727                                                                                                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh.eeeeeeeeeeeeeeeee..eeeeeeeeeeeeeeeeeee..eeeeeee....hhhhhhhhhhhhhhh.----...................hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeeeeeeeeeeeeeee....eeeeeeeeeeeeeeeee.....eeeeeeeee.hhhhhhhhhhhhhhhhhhhhh........eeeeeeehhhhhhhhh..hhhhhhhhhhhh...................eeee.....................eeeee..ee.....hhhhhhhhh......ee..ee...eeee.....hhhhhhhhhh.eeeeeeeehhhhhh.....eeeeeeeeeeee..eeeeeeeeeeeeeehhhhhhheeee....ee...eee..eeeeeeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vl4 A   1 MTFEEFKDRLFALAKKNGVEVQISFLETREFSLRLANGDLDQYTDAGKFNVEIKVLKDGKTGTFRTQVLENPEKCFEEALSNLQVK----KEYFFEGGKEYREMETYVGRFEKLSVKEKMDMAKKAHESAAKDERVVMVPTVMYKDMVIKKIITNTLGLDVESQMDGGFLFAMAIARDANPRSGSWYELARTPEDLNPEEIGKRAAEEAISLIGSKTIPSGKYPVLMRNTALLDLMEMFIPMISAENVQKNLSPLKGKLGEQVGNPAVSIKDLPYHPKGLSSTPFDDEGVPTTEKFVLENGVLKTFLHNLKTARKEGVEPTGNGFVGGIRPVNLMLMPGEKSFEELLKEMDRGVVITEVEGMHAGANSISGEFSLFAKGYWVENGEIAHGVEDITISGNFLDLLRKIVLVGNDVKVSQHTIAPSVLVEVLDVA 433
                                    10        20        30        40        50        60        70        80     |   -|      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   
                                                                                                                86   91                                                                                                                                                                                                                                                                                                                                                      


Chain B from PDB  Type:PROTEIN  Length:429
 aligned with Q9WZI6_THEMA | Q9WZI6 from UniProtKB/TrEMBL  Length:435

    Alignment length:433
                                    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   
         Q9WZI6_THEMA     1 MTFEEFKDRLFALAKKNGVEVQISFLETREFSLRLANGDLDQYTDAGKFNVEIKVLKDGKTGTFRTQVLENPEKCFEEALSNLQVKDSEEKEYFFEGGKEYREMETYVGRFEKLSVKEKMDMAKKAHESAAKDERVVMVPTVMYKDMVIKKIITNTLGLDVESQMDGGFLFAMAIARDANPRSGSWYELARTPEDLNPEEIGKRAAEEAISLIGSKTIPSGKYPVLMRNTALLDLMEMFIPMISAENVQKNLSPLKGKLGEQVGNPAVSIKDLPYHPKGLSSTPFDDEGVPTTEKFVLENGVLKTFLHNLKTARKEGVEPTGNGFVGGIRPVNLMLMPGEKSFEELLKEMDRGVVITEVEGMHAGANSISGEFSLFAKGYWVENGEIAHGVEDITISGNFLDLLRKIVLVGNDVKVSQHTIAPSVLVEVLDVA 433
               SCOP domains d1vl4b_ B: PmbA-related protein TM0727                                                                                                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ------------------PmbA_TldD-1vl4B01 B:19-306                                                                                                                                                                                                                                                                      ------------------------------------------------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ------------------PmbA_TldD-1vl4B02 B:19-306                                                                                                                                                                                                                                                                      ------------------------------------------------------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author .hhhhhhhhhhhhhhhhh.eeeeeeeeeeeeeeeee..eeeeeeeeeeeeeeeeeee..eeeeeee....hhhhhhhhhhhhhhh.----...................hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeeeeeeeeeeeeeee....eeeeeeeeeeeeeeeee.....eeeeeeeee.hhhhhhhhhhhhhhhhhhhh.........eeeeeeehhhhhhhhh.hhhhhhhhhhhhh...................eeee.....................eeeee..ee.....hhhhhhhhh......ee..ee...eeee.....hhhhhhhhhh.eeeeeeeehhhhhh.....eeeeeeeeeeee..eeeeee...eeeeehhhhhhheeee....ee...eee..eeeeeeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vl4 B   1 MTFEEFKDRLFALAKKNGVEVQISFLETREFSLRLANGDLDQYTDAGKFNVEIKVLKDGKTGTFRTQVLENPEKCFEEALSNLQVK----KEYFFEGGKEYREMETYVGRFEKLSVKEKMDMAKKAHESAAKDERVVMVPTVMYKDMVIKKIITNTLGLDVESQMDGGFLFAMAIARDANPRSGSWYELARTPEDLNPEEIGKRAAEEAISLIGSKTIPSGKYPVLMRNTALLDLMEMFIPMISAENVQKNLSPLKGKLGEQVGNPAVSIKDLPYHPKGLSSTPFDDEGVPTTEKFVLENGVLKTFLHNLKTARKEGVEPTGNGFVGGIRPVNLMLMPGEKSFEELLKEMDRGVVITEVEGMHAGANSISGEFSLFAKGYWVENGEIAHGVEDITISGNFLDLLRKIVLVGNDVKVSQHTIAPSVLVEVLDVA 433
                                    10        20        30        40        50        60        70        80     |   -|      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   
                                                                                                                86   91
   Legend:   → Mismatch (orange background)
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  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)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1VL4)

(-) Pfam Domains  (1, 2)

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

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q9WZI6_THEMA | Q9WZI6)
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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