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(-) Description

Title :  CRYSTAL STRUCTURE OF THE HYPAB-NI 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 :  1.63
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  (7, 11)

Asymmetric Unit (7, 11)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2CL1Ligand/IonCHLORIDE ION
3GOL2Ligand/IonGLYCEROL
4MG2Ligand/IonMAGNESIUM ION
5NI1Ligand/IonNICKEL (II) ION
6URE3Ligand/IonUREA
7ZN1Ligand/IonZINC ION
Biological Unit 1 (3, 12)
No.NameCountTypeFull Name
1ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE
2CL-1Ligand/IonCHLORIDE ION
3GOL4Ligand/IonGLYCEROL
4MG-1Ligand/IonMAGNESIUM ION
5NI-1Ligand/IonNICKEL (II) ION
6URE6Ligand/IonUREA
7ZN-1Ligand/IonZINC ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWARECYS A:73 , CYS A:76 , CYS A:110 , CYS A:113binding site for residue ZN A 201
02AC2SOFTWAREMET A:1 , HIS A:2 , GLU A:3 , HIS A:98binding site for residue NI A 202
03AC3SOFTWAREGLU A:35 , LEU A:36 , ASP A:38 , LYS A:94binding site for residue URE A 203
04AC4SOFTWAREGLU A:41 , PHE A:64 , HOH A:356 , HOH A:387binding site for residue URE A 204
05AC5SOFTWAREILE A:131 , LYS A:132 , HOH A:380 , LYS B:234 , GLU B:236binding site for residue URE A 205
06AC6SOFTWAREGLN A:19 , THR A:55 , ILE A:56 , HOH A:429binding site for residue CL A 206
07AC7SOFTWAREASP B:5binding site for residue GOL A 207
08AC8SOFTWARELYS B:28 , GLY B:30 , VAL B:31 , GLY B:32 , LYS B:33 , SER B:34 , LEU B:35 , SER B:160 , LEU B:162 , ASN B:187 , MET B:188 , PRO B:217 , PHE B:218 , TYR B:219 , LEU B:222 , PHE B:237 , MG B:302 , HOH B:411 , HOH B:412 , HOH B:421 , HOH B:423 , HOH B:489 , HOH B:519 , HOH B:538binding site for residue ADP B 301
09AC9SOFTWARESER B:34 , ADP B:301 , HOH B:421 , HOH B:422 , HOH B:423 , HOH B:519binding site for residue MG B 302
10AD1SOFTWAREHOH A:310 , HOH A:323 , LYS B:149 , HOH B:416 , HOH B:473 , HOH B:550binding site for residue MG B 303
11AD2SOFTWARETRP A:4 , TYR A:78 , ARG B:79 , HOH B:420binding site for residue GOL B 304

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5AUN)

(-) 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
                 5aun 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 ........hhhhhhh..eeeeeeee......hhhhhhhhhhhhhhhh...eeeee......hhhhhhh................ee..eeeee.hhhh.......hhhhhhhhhhhhhhhh....eeeeeee.....hhhhhhhhhhh...eeeeee..hhhhhhhhhhhhhhhhhh..eeeeeeeeee..hhhhhhhhh...eeeeee...hhhhh..hhhhhh.hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5aun 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
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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 5AUN)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (8, 9)

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 Related Entries

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

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