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(-) Description

Title :  CRYSTAL STRUCTURE OF THE HYPAB-NI COMPLEX (AMPPCP)
 
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 :  1.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
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
    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
    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

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 7)

Asymmetric Unit (6, 7)
No.NameCountTypeFull Name
1ACP1Ligand/IonPHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
2CL1Ligand/IonCHLORIDE ION
3GOL1Ligand/IonGLYCEROL
4MG2Ligand/IonMAGNESIUM ION
5NI1Ligand/IonNICKEL (II) ION
6ZN1Ligand/IonZINC ION
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1ACP2Ligand/IonPHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
2CL-1Ligand/IonCHLORIDE ION
3GOL2Ligand/IonGLYCEROL
4MG-1Ligand/IonMAGNESIUM ION
5NI-1Ligand/IonNICKEL (II) ION
6ZN-1Ligand/IonZINC ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:73 , CYS A:76 , CYS A:110 , CYS A:113binding site for residue ZN A 201
2AC2SOFTWAREMET A:1 , HIS A:2 , GLU A:3 , HIS A:98binding site for residue NI A 202
3AC3SOFTWAREGLN A:19 , THR A:55 , ILE A:56binding site for residue CL A 203
4AC4SOFTWARELYS B:28 , GLY B:29 , GLY B:30 , VAL B:31 , GLY B:32 , LYS B:33 , SER B:34 , LEU B:35 , ASP B:57 , PRO B:135 , SER B:160 , LEU B:162 , ASN B:187 , MET B:188 , PRO B:217 , PHE B:218 , TYR B:219 , MG B:302 , HOH B:414 , HOH B:436 , HOH B:454binding site for residue ACP B 301
5AC5SOFTWARESER B:34 , ACP B:301 , HOH B:422 , HOH B:436 , HOH B:454binding site for residue MG B 302
6AC6SOFTWAREHOH A:316 , HOH A:355 , LYS B:149 , HOH B:408 , HOH B:425 , HOH B:490binding site for residue MG B 303
7AC7SOFTWAREPRO A:111 , LYS A:112 , ARG B:79binding site for residue GOL B 304

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5AUO)

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


Chain B from PDB  Type:PROTEIN  Length:237
                                                                                                                                                                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhh..eeeeeeee......hhhhhhhhhhhhhhhh...eeeee......hhhhhhh.......ee...ee..ee..eeeee.hhhh.......hhhhhhhhhhhhhhhh....eeeeeee.....hhhhhhhhhhh...eeeeee..hhhhhhhhhhhhhhhhhh..eeeeeeeeee..hhhhhhhhhh..eeeeee...hhhhh..hhhhhh.hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5auo B   4 IDPREIAINARLEGVKRIIPVVSGKGGVGKSLVSTTLALVLAEKGYRVGLLDLDFHGASDHVILGFEPKEFPEEDRGVVPPTVHGIKFMTIAYYTEDRPTPLRGKEISDALIELLTITRWDELDYLVIDMPPGLGDQLLDVLRFLKRGEFLVVATPSKLSLNVVRKLIELLKEEGHKVIGVVENMKLKDVEKLAEEFGVPYLVGIPFYPDLDAKVGNVEELMKTEFAGKVRELAGRL 248
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183      |201       211       221       231       241       
                                                                                                                                                                                                                    190|                                                 
                                                                                                                                                                                                                     199
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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 5AUO)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (8, 9)

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  5auo
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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 5aup
UniProtKB/TrEMBL
        Q5JIH4_THEKO | Q5JIH4: 3vx3 5aun 5aup 5auq

(-) Related Entries Specified in the PDB File

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