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(-) Description

Title :  CRYSTAL STRUCTURE OF THE HYPAB COMPLEX
 
Authors :  S. Watanabe, T. Kawashima, Y. Nishitani, K. Miki
Date :  27 May 15  (Deposition) - 24 Jun 15  (Release) - 08 Jul 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.10
Chains :  Asym./Biol. Unit :  A,B,H,I
Keywords :  Protein Complex, Metallochaperone (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Watanabe, T. Kawashima, Y. Nishitani, T. Kanai, T. Wada, K. Inaba, H. Atomi, T. Imanaka, K. Miki
Structural Basis Of A Ni Acquisition Cycle For [Nife] Hydrogenase By Ni-Metallochaperone Hypa And Its Enhancer
Proc. Natl. Acad. Sci. Usa V. 112 7701 2015
PubMed-ID: 26056269  |  Reference-DOI: 10.1073/PNAS.1503102112

(-) Compounds

Molecule 1 - PROBABLE HYDROGENASE NICKEL INCORPORATION PROTEIN HYPA
    Chains: A, H
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: HYPA, TK2008
    Organism Scientific: THERMOCOCCUS KODAKARAENSIS (STRAIN ATCC BAA-918 / JCM 12380 / KOD1)
    Organism Taxid: 69014
    Strain: ATCC BAA-918 / JCM 12380 / KOD1
 
Molecule 2 - ATPASE INVOLVED IN CHROMOSOME PARTITIONING, PARA/MIND FAMILY, MRP HOMOLOG
    Chains: B, I
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: TK2007
    Organism Scientific: THERMOCOCCUS KODAKARAENSIS (STRAIN ATCC BAA-918 / JCM 12380 / KOD1)
    Organism Taxid: 69014
    Strain: ATCC BAA-918 / JCM 12380 / KOD1
    Synonym: HYPB

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABHI

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
1ACP2Ligand/IonPHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
2MG2Ligand/IonMAGNESIUM ION
3ZN2Ligand/IonZINC ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:73 , CYS A:76 , CYS A:110 , CYS A:113binding site for residue ZN A 201
2AC2SOFTWAREGLY B:30 , VAL B:31 , GLY B:32 , LYS B:33 , SER B:34 , LEU B:35 , ASP B:57 , PRO B:135 , ASN B:187 , MET B:188 , PRO B:217 , TYR B:219 , LEU B:222 , ASP B:223 , PHE B:237 , MG B:302 , HOH B:401 , HOH B:402 , HOH B:403 , LYS I:28 , GLY I:29 , SER I:160 , LEU I:162binding site for residue ACP B 301
3AC3SOFTWARESER B:34 , ACP B:301 , HOH B:401 , HOH B:402 , HOH B:403binding site for residue MG B 302
4AC4SOFTWARECYS H:73 , CYS H:76 , CYS H:110 , CYS H:113binding site for residue ZN H 201
5AC5SOFTWARELYS B:28 , GLY B:29 , SER B:160 , GLY I:29 , GLY I:30 , GLY I:32 , LYS I:33 , SER I:34 , LEU I:35 , ASP I:57 , PRO I:135 , ASN I:187 , MET I:188 , PRO I:217 , TYR I:219 , ASP I:223 , MG I:302 , HOH I:401 , HOH I:402 , HOH I:403binding site for residue ACP I 301
6AC6SOFTWARESER I:34 , ASP I:57 , ACP I:301 , HOH I:401 , HOH I:402 , HOH I:403binding site for residue MG I 302

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5AUP)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5AUP)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5AUP)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5AUP)

(-) Exons   (0, 0)

(no "Exon" information available for 5AUP)

(-) 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:136
                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhh...eeeeeeeeee.....hhhhhhhhhhhhhh.......eeeeeee..eeee.....eee.hhhhhhhhhhhhhhhhhhhhhhhhh..........eeeee...eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5aup A   1 MHEWALADAIVRTVLDYAQREGASRVKAVRVVLGELQDVAEDIVKFAMEQLFAGTIAEGAEIEFVEEEAVFKCRNCNYEWKLKEVKDKFDERIKEDIHFIPEVVHAFLACPKCGSHDFEVVKGRGVYVAGIKIEKE 136
                                    10        20        30        40        50        60        70        80        90       100       110       120       130      


Chain B from PDB  Type:PROTEIN  Length:240
                                                                                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......hhhhhhhhh..eeeeeeee......hhhhhhhhhhhhhhhh...eeeee......hhhhhh........ee...ee......eeee.............hhhhhhhhhhhhhhhh....eeeeeee.....hhhhhhhhhhh....eeeee..hhhhhhhhhhhhhhhhhhh..eeeeeeeee..hhhhhhhhhh..eeeeee..........hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5aup B   1 MNAIDPREIAINARLEGVKRIIPVVSGKGGVGKSLVSTTLALVLAEKGYRVGLLDLDFHGASDHVILGFEPKEFPEEDRGVVPPTVHGIKFMTIAYYTEDRPTPLRGKEISDALIELLTITRWDELDYLVIDMPPGLGDQLLDVLRFLKRGEFLVVATPSKLSLNVVRKLIELLKEEGHKVIGVVENMKLKDVEKLAEEFGVPYLVGIPFYPDLDAKVGNVEELMKTEFAGKVRELAGRL 248
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190|      208       218       228       238       248
                                                                                                                                                                                                                       190|                                                 
                                                                                                                                                                                                                        199                                                 


Chain H from PDB  Type:PROTEIN  Length:135
                                                                                                                                                                       
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhh.....eeeeeeeeee.....hhhhhhhhhhhhhh.......eeeeeee..eeee.....eee...hhhhhhhhhhhhhhhh..hhhhhh.........eeeee...eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5aup H   1 MHEWALADAIVRTVLDYAQREGASRVKAVRVVLGELQDVAEDIVKFAMEQLFAGTIAEGAEIEFVEEEAVFKCRNCNYEWKLKEVKDKFDERIKEDIHFIPEVVHAFLACPKCGSHDFEVVKGRGVYVAGIKIEK 135
                                    10        20        30        40        50        60        70        80        90       100       110       120       130     


Chain I from PDB  Type:PROTEIN  Length:241
                                                                                                                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhh..eeeeeeee......hhhhhhhhhhhhhhhh...eeeee......hhhhhhh....................eeee.............hhhhhhhhhhhhhhhh....eeeeeee.....hhhhhhhhhhh....eeeee..hhhhhhhhhhhhhhhhhhh..eeeeeeeee...hhhhhhhhhh..eeeeee...hhhhh..hhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5aup I   1 MNAIDPREIAINARLEGVKRIIPVVSGKGGVGKSLVSTTLALVLAEKGYRVGLLDLDFHGASDHVILGFEPKEFPEEDRGVVPPTVHGIKFMTIAYYTEDRPTPLRGKEISDALIELLTITRWDELDYLVIDMPPGLGDQLLDVLRFLKRGEFLVVATPSKLSLNVVRKLIELLKEEGHKVIGVVENMKLRKDVEKLAEEFGVPYLVGIPFYPDLDAKVGNVEELMKTEFAGKVRELAGRL 248
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190||     207       217       227       237       247 
                                                                                                                                                                                                                        191|                                                 
                                                                                                                                                                                                                         199
   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  (0, 0)

(no "SCOP Domain" information available for 5AUP)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5AUP)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5AUP)

(-) Gene Ontology  (8, 9)

Asymmetric/Biological Unit(hide GO term definitions)

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  5aup
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  HYPA_THEKO | Q5JIH3
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  Q5JIH4_THEKO | Q5JIH4
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        HYPA_THEKO | Q5JIH3: 3a43 3a44 5aun 5auo
UniProtKB/TrEMBL
        Q5JIH4_THEKO | Q5JIH4: 3vx3 5aun 5auo 5auq

(-) Related Entries Specified in the PDB File

3a43 3A43 IS A ISOLATED STRUCTURE OF THE SAME PROTEIN.
3vx3 3VX3 IS A ISOLATED STRUCTURE OF THE SAME PROTEIN.
5aun
5auo
5auq