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(-) Description

Title :  CRYSTAL STRUCTURE OF [NIFE] HYDROGENASE MATURATION PROTEIN HYPB FROM THERMOCOCCUS KODAKARENSIS KOD1
 
Authors :  D. Sasaki, S. Watanabe, K. Miki
Date :  09 Sep 12  (Deposition) - 27 Feb 13  (Release) - 12 Jun 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Mrp/Mind Family Atpase, [Nife] Hydrogenase Maturation, Adp Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Sasaki, S. Watanabe, R. Matsumi, T. Shoji, A. Yasukochi, K. Tagashira, W. Fukuda, T. Kanai, H. Atomi, T. Imanaka, K. Miki
Identification And Structure Of A Novel Archaeal Hypb For [Nife] Hydrogenase Maturation
J. Mol. Biol. V. 425 1627 2013
PubMed-ID: 23399544  |  Reference-DOI: 10.1016/J.JMB.2013.02.004

(-) Compounds

Molecule 1 - ATPASE INVOLVED IN CHROMOSOME PARTITIONING, PARA/MIND FAMILY, MRP HOMOLOG
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21A(+)
    Expression System Strain: ROSETTA2(DE3)PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: TK2007
    Organism Scientific: THERMOCOCCUS KODAKARENSIS
    Organism Taxid: 69014
    Strain: ATCC BAA-918 / JCM 12380 / KOD1

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric/Biological Unit (2, 8)
No.NameCountTypeFull Name
1ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE
2EDO6Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:30 , VAL A:31 , GLY A:32 , LYS A:33 , SER A:34 , LEU A:35 , ASN A:187 , PRO A:217 , PHE A:218 , TYR A:219 , ASP A:223 , HOH A:411 , HOH A:414 , HOH A:436 , LYS B:28 , SER B:160 , LEU B:162BINDING SITE FOR RESIDUE ADP A 301
2AC2SOFTWARELYS A:28 , GLY A:29 , LYS B:28 , GLY B:29BINDING SITE FOR RESIDUE EDO A 302
3AC3SOFTWAREASP A:139 , HOH A:473 , GLY B:107 , ILE B:110 , ASP B:139 , GLN B:140BINDING SITE FOR RESIDUE EDO A 303
4AC4SOFTWAREGLY A:68 , GLY A:227 , ASN A:228 , HOH A:470BINDING SITE FOR RESIDUE EDO A 304
5AC5SOFTWARELYS A:28 , SER A:160 , LEU A:162 , GLY B:29 , GLY B:30 , VAL B:31 , GLY B:32 , LYS B:33 , SER B:34 , LEU B:35 , ASN B:187 , MET B:188 , PRO B:217 , PHE B:218 , TYR B:219 , ASP B:223 , VAL B:226 , HOH B:408 , HOH B:414 , HOH B:422 , HOH B:433 , HOH B:443BINDING SITE FOR RESIDUE ADP B 301
6AC6SOFTWARETYR B:219 , PRO B:220 , ASP B:221 , LEU B:222 , LYS B:225 , HOH B:415 , HOH B:463BINDING SITE FOR RESIDUE EDO B 302
7AC7SOFTWARELYS B:175 , LYS B:180 , VAL B:181 , GLY B:209BINDING SITE FOR RESIDUE EDO B 303
8AC8SOFTWAREGLU A:176 , TYR B:97 , ALA B:113 , GLU B:116 , LEU B:117 , ILE B:120BINDING SITE FOR RESIDUE EDO B 304

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3VX3)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Thr B:103 -Pro B:104

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3VX3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3VX3)

(-) Exons   (0, 0)

(no "Exon" information available for 3VX3)

(-) 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:235
 aligned with Q5JIH4_THEKO | Q5JIH4 from UniProtKB/TrEMBL  Length:248

    Alignment length:245
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243     
         Q5JIH4_THEKO     4 IDPREIAINARLEGVKRIIPVVSGKGGVGKSLVSTTLALVLAEKGYRVGLLDLDFHGASDHVILGFEPKEFPEEDRGVVPPTVHGIKFMTIAYYTEDRPTPLRGKEISDALIELLTITRWDELDYLVIDMPPGLGDQLLDVLRFLKRGEFLVVATPSKLSLNVVRKLIELLKEEGHKVIGVVENMKLRSEQLDDEKDVEKLAEEFGVPYLVGIPFYPDLDAKVGNVEELMKTEFAGKVRELAGRL 248
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh.eeeeeeeee.....hhhhhhhhhhhhhhhh...eeeee......hhhhhh........ee..ee...ee..eeeee.hhh.----...hhhhhhhhhhhhhhhh....eeeeeee.....hhhhhhhhh.....eeeeee.....hhhhhhhhhhhhhhh..eeeeeeeeee..------.hhhhhhhhhh...eeeeee...hhhhhh.hhhhhh.hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vx3 A   4 IDPREIAINARLEGVKRIIPVVSGKGGVGKSLVSTTLALVLAEKGYRVGLLDLDFHGASDHVILGFEPKEFPEEDRGVVPPTVHGIKFMTIAYYT----TPLRGKEISDALIELLTITRWDELDYLVIDMPPGLGDQLLDVLRFLKRGEFLVVATPSKLSLNVVRKLIELLKEEGHKVIGVVENMKLR------EKDVEKLAEEFGVPYLVGIPFYPDLDAKVGNVEELMKTEFAGKVRELAGRL 248
                                    13        23        33        43        53        63        73        83        93    |  103       113       123       133       143       153       163       173       183       | -    |  203       213       223       233       243     
                                                                                                                         98  103                                                                                     191    198                                                  


Chain B from PDB  Type:PROTEIN  Length:235
 aligned with Q5JIH4_THEKO | Q5JIH4 from UniProtKB/TrEMBL  Length:248

    Alignment length:245
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243     
         Q5JIH4_THEKO     4 IDPREIAINARLEGVKRIIPVVSGKGGVGKSLVSTTLALVLAEKGYRVGLLDLDFHGASDHVILGFEPKEFPEEDRGVVPPTVHGIKFMTIAYYTEDRPTPLRGKEISDALIELLTITRWDELDYLVIDMPPGLGDQLLDVLRFLKRGEFLVVATPSKLSLNVVRKLIELLKEEGHKVIGVVENMKLRSEQLDDEKDVEKLAEEFGVPYLVGIPFYPDLDAKVGNVEELMKTEFAGKVRELAGRL 248
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh.eeeeeeeee.....hhhhhhhhhhhhhhhh...eeeee......hhhhhh.................ee..eeeee.hhhh----....hhhhhhhhhhhhhhh....eeeeeee.....hhhhhhhhh.....eeeeee..hhhhhhhhhhhhhhhhhh..eeeeeeeeee..------.hhhhhhhhhh...eeeeee...hhhhh..hhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vx3 B   4 IDPREIAINARLEGVKRIIPVVSGKGGVGKSLVSTTLALVLAEKGYRVGLLDLDFHGASDHVILGFEPKEFPEEDRGVVPPTVHGIKFMTIAYYT----TPLRGKEISDALIELLTITRWDELDYLVIDMPPGLGDQLLDVLRFLKRGEFLVVATPSKLSLNVVRKLIELLKEEGHKVIGVVENMKLR------EKDVEKLAEEFGVPYLVGIPFYPDLDAKVGNVEELMKTEFAGKVRELAGRL 248
                                    13        23        33        43        53        63        73        83        93    |  103       113       123       133       143       153       163       173       183       | -    |  203       213       223       233       243     
                                                                                                                         98  103                                                                                     191    198
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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  (0, 0)

(no "SCOP Domain" information available for 3VX3)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3VX3)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3VX3)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q5JIH4_THEKO | Q5JIH4)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0016887    ATPase activity    Catalysis of the reaction: ATP + H2O = ADP + phosphate + 2 H+. May or may not be coupled to another reaction.
    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:0051536    iron-sulfur cluster binding    Interacting selectively and non-covalently with an iron-sulfur cluster, a combination of iron and sulfur atoms.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.

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 Related Entries

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UniProtKB/TrEMBL
        Q5JIH4_THEKO | Q5JIH4: 5aun 5auo 5aup 5auq

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