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(-) Description

Title :  CRYSTAL STRUCTURE OF THE HYPC-HYPD-HYPE COMPLEX (FORM I INWARD)
 
Authors :  S. Watanabe, K. Miki
Date :  02 Oct 12  (Deposition) - 28 Nov 12  (Release) - 31 Jul 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.25
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B,C  (2x)
Keywords :  [Nife] Hydrogenase Maturation, Metal Binding Protein-Transferase Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Watanabe, R. Matsumi, H. Atomi, T. Imanaka, K. Miki
Crystal Structures Of The Hypcd Complex And The Hypcde Ternary Complex: Transient Intermediate Complexes During [Nife] Hydrogenase Maturation
Structure V. 20 2124 2012
PubMed-ID: 23123111  |  Reference-DOI: 10.1016/J.STR.2012.09.018

(-) Compounds

Molecule 1 - HYDROGENASE EXPRESSION/FORMATION PROTEIN HYPC
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: TK-HYPC
    Organism Scientific: THERMOCOCCUS KODAKARENSIS
    Organism Taxid: 69014
    Strain: KOD1
 
Molecule 2 - HYDROGENASE EXPRESSION/FORMATION PROTEIN HYPD
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: TK-HYPD
    Organism Scientific: THERMOCOCCUS KODAKARENSIS
    Organism Taxid: 69014
    Strain: KOD1
 
Molecule 3 - HYDROGENASE EXPRESSION/FORMATION PROTEIN HYPE
    Chains: C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: TK1993
    Organism Scientific: THERMOCOCCUS KODAKARENSIS
    Organism Taxid: 69014
    Strain: KOD1

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (2x): ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 7)

Asymmetric Unit (3, 7)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2MG5Ligand/IonMAGNESIUM ION
3SF41Ligand/IonIRON/SULFUR CLUSTER
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2MG-1Ligand/IonMAGNESIUM ION
3SF42Ligand/IonIRON/SULFUR CLUSTER

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS B:323 , ARG B:324 , CYS B:325 , CYS B:338 , CYS B:345 , GLY B:352 , MET B:355 , CYS B:362BINDING SITE FOR RESIDUE SF4 B 501
2AC2SOFTWAREASP C:59 , ASP C:84 , MG C:602 , CL C:604 , MG C:605 , MG C:606 , HOH C:701 , HOH C:783BINDING SITE FOR RESIDUE MG C 601
3AC3SOFTWAREASP C:43 , ASP C:84 , ASP C:221 , MG C:601 , MG C:605 , HOH C:701 , HOH C:719 , HOH C:721BINDING SITE FOR RESIDUE MG C 602
4AC4SOFTWAREASP C:42 , ASP C:43 , ASP C:158 , MET C:219 , HOH C:722BINDING SITE FOR RESIDUE MG C 603
5AC5SOFTWARETHR C:223 , MG C:601 , MG C:606BINDING SITE FOR RESIDUE CL C 604
6AC6SOFTWAREASP C:43 , ASP C:84 , MG C:601 , MG C:602 , MG C:606 , HOH C:713 , HOH C:721BINDING SITE FOR RESIDUE MG C 605
7AC7SOFTWAREASP C:59 , ASP C:132 , MG C:601 , CL C:604 , MG C:605 , HOH C:713BINDING SITE FOR RESIDUE MG C 606

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1B:66 -B:69
2B:325 -B:354

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Lys C:64 -Pro C:65
2Val C:124 -Pro C:125

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3VYT)

(-) 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:52
 aligned with Q5JII0_THEKO | Q5JII0 from UniProtKB/TrEMBL  Length:75

    Alignment length:52
                                    12        22        32        42        52  
         Q5JII0_THEKO     3 LAVPGKVIEVNGPVAVVDFGGVKREVRLDLMPDTKPGDWVIVHTGFAIEKLD  54
               SCOP domains d3vyta_ A:                                           SCOP domains
               CATH domains ---------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeee..eeeee....eeeee...........eeeee..eeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------- Transcript
                 3vyt A   3 LAVPGKVIEVNGPVAVVDFGGVKREVRLDLMPDTKPGDWVIVHTGFAIEKLD  54
                                    12        22        32        42        52  


Chain B from PDB  Type:PROTEIN  Length:368
 aligned with Q5JII1_THEKO | Q5JII1 from UniProtKB/TrEMBL  Length:372

    Alignment length:368
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363        
         Q5JII1_THEKO     4 PFEAYRSREVAMKLVEKIREEAKTLDGEIRIMHVCGTHEDTVTRHGIRSLLPENVKVVSGPGCPVCITPVEDIVAMQLIMRKAREEGEEIILTTFGDMYKIPTPMGSFADLKSEGFDVRIVYGIFDTYRIAKENPDKTVVHFSPGFETTTAPAAGMLNVAAQEELENFKIYSVHRLTPPAVEVLLKQGTVFQGLIAPGHVSTIIGVKGWEYLTEKYGIPQVVAGFEPNDVLMAILMLIRMYKEGEARIINEYERAVKYEGNVVAQKMIDKFFEVVDAKWRALGVFPKSGLELRKEWKDFEIRSFYKVEVPKNLPDLEKGCRCGAVLRGLALPTDCPLFGKTCTPRHPVGPCMVSYEGTCQIFYKYGVL 371
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhh....eeeee.hhhhhhhhhhhhhhhhh...eeeee.........hhhhhhhhhhhhhhhhhh...eeeeehhhhhhh.....hhhhhhh...eeee..hhhhhhhhhhhh...eeeeeeeehhhhhhhhhhhhhhhhhh....eeeeeeeehhhhhhhhhhhh.....eee.hhhhhhhhhhhhhhhhhhhh...eee...hhhhhhhhhhhhhhhhhh....eee..........hhhhhhhhhh.eeeeeeee...eeeeeeeeee.hhhhhhhhhhh................hhhhhhh...hhhhh.............hhhhhh..hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vyt B   4 PFEAYRSREVAMKLVEKIREEAKTLDGEIRIMHVCGTHEDTVTRHGIRSLLPENVKVVSGPGCPVCITPVEDIVAMQLIMRKAREEGEEIILTTFGDMYKIPTPMGSFADLKSEGFDVRIVYGIFDTYRIAKENPDKTVVHFSPGFETTTAPAAGMLNVAAQEELENFKIYSVHRLTPPAVEVLLKQGTVFQGLIAPGHVSTIIGVKGWEYLTEKYGIPQVVAGFEPNDVLMAILMLIRMYKEGEARIINEYERAVKYEGNVVAQKMIDKFFEVVDAKWRALGVFPKSGLELRKEWKDFEIRSFYKVEVPKNLPDLEKGCRCGAVLRGLALPTDCPLFGKTCTPRHPVGPCMVSYEGTCQIFYKYGVL 371
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363        


Chain C from PDB  Type:PROTEIN  Length:336
 aligned with Q5JII7_THEKO | Q5JII7 from UniProtKB/TrEMBL  Length:338

    Alignment length:336
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332      
         Q5JII7_THEKO     3 EKIKLEHGAGGEIMEELLRDVILKTLTLKSAGGIGLDALDDGATIPFGDKHIVFTIDGHTVKPLFFPGGDIGRLAVSGTVNDLAVMGAEPIALANSMIIGEGLDMEVLKRVLKSMDETAREVPVPIVTGDTKVVEDKIEMFVITAGIGIAEHPVSDAGAKVGDAVLVSGTIGDHGIALMSHREGIAFETELKSDVAPIWDVVKAVAETIGWENIHAMKDPTRAGLSNALNEIARKSNVGILVREADIPIRPEVRAASEMLGISPYDVANEGKVVMVVAREYAEEALEAMRKTEKGRNAAIIGEVIADYRGKVLLETGIGGKRFMEPPEGDPVPRIC 338
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhh.hhhhhhhhhhhhhhhh........hhhhh...eeeee..eeeeeeeeee.....ee..eehhhhhhhhhhhhhhh...eeeeeeeeeeee...hhhhhhhhhhhhhhhhhhh...eeeeeeeee.....eeeeeeeeeee.............eeee....hhhhhhhhhhhh..............hhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhh.eeeee.hhh..hhhhhhhhhhhh............eeee...hhhhhhhhhhh.......eeeeeee......eeee.....eee............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3vyt C   3 EKIKLEHGAGGEIMEELLRDVILKTLTLKSAGGIGLDALDDGATIPFGDKHIVFTIDGHTVKPLFFPGGDIGRLAVSGTVNDLAVMGAEPIALANSMIIGEGLDMEVLKRVLKSMDETAREVPVPIVTGDTKVVEDKIEMFVITAGIGIAEHPVSDAGAKVGDAVLVSGTIGDHGIALMSHREGIAFETELKSDVAPIWDVVKAVAETIGWENIHAMKDPTRAGLSNALNEIARKSNVGILVREADIPIRPEVRAASEMLGISPYDVANEGKVVMVVAREYAEEALEAMRKTEKGRNAAIIGEVIADYRGKVLLETGIGGKRFMEPPEGDPVPRIC 338
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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, 1)

Asymmetric Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (5, 6)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q5JII0_THEKO | Q5JII0)

Chain B   (Q5JII1_THEKO | Q5JII1)
molecular function
    GO:0051539    4 iron, 4 sulfur cluster binding    Interacting selectively and non-covalently with a 4 iron, 4 sulfur (4Fe-4S) cluster; this cluster consists of four iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands.
    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.

Chain C   (Q5JII7_THEKO | Q5JII7)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    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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  3vyt
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 Related Entries

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

UniProtKB/TrEMBL
        Q5JII0_THEKO | Q5JII0: 2z1c 3vyr 3vys 3vyu
        Q5JII1_THEKO | Q5JII1: 2z1d 3vyr 3vys 3vyu
        Q5JII7_THEKO | Q5JII7: 2z1e 2z1f 3vys 3vyu 3wjp 3wjq 3wjr

(-) Related Entries Specified in the PDB File

2z1c 2z1d 2z1e 3vyr 3vys 3vyu