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(-) Description

Title :  CRYSTAL STRUCTURE OF [NIFE] HYDROGENASE MATURATION PROTEIN, HYPD FROM THERMOCOCCUS KODAKARAENSIS
 
Authors :  S. Watanabe, R. Matsumi, T. Arai, H. Atomi, T. Imanaka, K. Miki
Date :  08 May 07  (Deposition) - 17 Jul 07  (Release) - 12 Nov 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.07
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  [Nife] Hydrogenase Maturation, [4Fe-4S] Cluster, Thiol Redox, Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Watanabe, R. Matsumi, T. Arai, H. Atomi, T. Imanaka, K. Miki
Crystal Structures Of [Nife] Hydrogenase Maturation Protein Hypc, Hypd, And Hype: Insights Into Cyanation Reaction By Thiol Redox Signaling
Mol. Cell V. 27 29 2007
PubMed-ID: 17612488  |  Reference-DOI: 10.1016/J.MOLCEL.2007.05.039

(-) Compounds

Molecule 1 - HYDROGENASE EXPRESSION/FORMATION PROTEIN HYPD
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: HYPD
    Organism Scientific: THERMOCOCCUS KODAKARENSIS
    Organism Taxid: 69014
    Strain: KOD1

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1CSD2Mod. Amino Acid3-SULFINOALANINE
2SF42Ligand/IonIRON/SULFUR CLUSTER
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1CSD1Mod. Amino Acid3-SULFINOALANINE
2SF41Ligand/IonIRON/SULFUR CLUSTER
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1CSD1Mod. Amino Acid3-SULFINOALANINE
2SF41Ligand/IonIRON/SULFUR CLUSTER

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:323 , ARG A:324 , CYS A:325 , CYS A:338 , CYS A:345 , GLY A:352 , CYS A:354 , MET A:355 , CYS A:362BINDING SITE FOR RESIDUE SF4 A 501
2AC2SOFTWARECYS B:323 , ARG B:324 , CYS B:325 , CYS B:338 , PHE B:341 , CYS B:345 , GLY B:352 , CYS B:354 , MET B:355 , CYS B:362BINDING SITE FOR RESIDUE SF4 B 502

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1A:66 -A:69
2A:325 -A:354
3B:66 -B:69
4B:325 -B:354

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2Z1D)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2Z1D)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2Z1D)

(-) Exons   (0, 0)

(no "Exon" information available for 2Z1D)

(-) 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:366
 aligned with Q5JII1_THEKO | Q5JII1 from UniProtKB/TrEMBL  Length:372

    Alignment length:366
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366      
         Q5JII1_THEKO     7 AYRSREVAMKLVEKIREEAKTLDGEIRIMHVCGTHEDTVTRHGIRSLLPENVKVVSGPGCPVCITPVEDIVAMQLIMRKAREEGEEIILTTFGDMYKIPTPMGSFADLKSEGFDVRIVYGIFDTYRIAKENPDKTVVHFSPGFETTTAPAAGMLNVAAQEELENFKIYSVHRLTPPAVEVLLKQGTVFQGLIAPGHVSTIIGVKGWEYLTEKYGIPQVVAGFEPNDVLMAILMLIRMYKEGEARIINEYERAVKYEGNVVAQKMIDKFFEVVDAKWRALGVFPKSGLELRKEWKDFEIRSFYKVEVPKNLPDLEKGCRCGAVLRGLALPTDCPLFGKTCTPRHPVGPCMVSYEGTCQIFYKYGVLF 372
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhh.....eeeee............hhhhhh...eeeee.........hhhhhhhhhhhhhhhhhh...eeeee..hhhhh.....hhhhhhhh..eeee..hhhhhhhhhhhh...eeeeeeeehhhhhhhhhhhhhhhhhhh...eeeeeeeehhhhhhhhhhhh.....eeeeehhhhhhhhhhhhhhhhhhhh..eeee..hhhhhhhhhhhhhhhhhh....eee..........hhhhhhhhhhheeeeeeee...eeeeeeeeee.hhhhhhhhhhh................hhhhhhh...hhhhh.............hhhhhh..hhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2z1d A   7 AYRSREVAMKLVEKIREEAKTLDGEIRIMHVcGTHEDTVTRHGIRSLLPENVKVVSGPGCPVCITPVEDIVAMQLIMRKAREEGEEIILTTFGDMYKIPTPMGSFADLKSEGFDVRIVYGIFDTYRIAKENPDKTVVHFSPGFETTTAPAAGMLNVAAQEELENFKIYSVHRLTPPAVEVLLKQGTVFQGLIAPGHVSTIIGVKGWEYLTEKYGIPQVVAGFEPNDVLMAILMLIRMYKEGEARIINEYERAVKYEGNVVAQKMIDKFFEVVDAKWRALGVFPKSGLELRKEWKDFEIRSFYKVEVPKNLPDLEKGCRCGAVLRGLALPTDCPLFGKTCTPRHPVGPCMVSYEGTCQIFYKYGVLF 372
                                    16        26        36 |      46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366      
                                                          38-CSD                                                                                                                                                                                                                                                                                                                                          


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

    Alignment length:368
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364        
         Q5JII1_THEKO     5 FEAYRSREVAMKLVEKIREEAKTLDGEIRIMHVCGTHEDTVTRHGIRSLLPENVKVVSGPGCPVCITPVEDIVAMQLIMRKAREEGEEIILTTFGDMYKIPTPMGSFADLKSEGFDVRIVYGIFDTYRIAKENPDKTVVHFSPGFETTTAPAAGMLNVAAQEELENFKIYSVHRLTPPAVEVLLKQGTVFQGLIAPGHVSTIIGVKGWEYLTEKYGIPQVVAGFEPNDVLMAILMLIRMYKEGEARIINEYERAVKYEGNVVAQKMIDKFFEVVDAKWRALGVFPKSGLELRKEWKDFEIRSFYKVEVPKNLPDLEKGCRCGAVLRGLALPTDCPLFGKTCTPRHPVGPCMVSYEGTCQIFYKYGVLF 372
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhh.....eeeee............hhhhhh...eeeee.........hhhhhhhhhhhhhhhhhh...eeeee..hhhhh.....hhhhhhhh..eeee..hhhhhhhhhhhh...eeeeeeeehhhhhhhhhhhhhhhhhhh...eeeeeeee.hhhhhhhhhhh.....eeeeehhhhhhhhhhhhhhhhhh....eeee..hhhhhhhhhhhhhhhhhh....eee..........hhhhhhhhhhheeeeeeee...eeeeeeeeee.hhhhhhhhhhh................hhhhhhh...hhhhh.............hhhhhh..hhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2z1d B   5 FEAYRSREVAMKLVEKIREEAKTLDGEIRIMHVcGTHEDTVTRHGIRSLLPENVKVVSGPGCPVCITPVEDIVAMQLIMRKAREEGEEIILTTFGDMYKIPTPMGSFADLKSEGFDVRIVYGIFDTYRIAKENPDKTVVHFSPGFETTTAPAAGMLNVAAQEELENFKIYSVHRLTPPAVEVLLKQGTVFQGLIAPGHVSTIIGVKGWEYLTEKYGIPQVVAGFEPNDVLMAILMLIRMYKEGEARIINEYERAVKYEGNVVAQKMIDKFFEVVDAKWRALGVFPKSGLELRKEWKDFEIRSFYKVEVPKNLPDLEKGCRCGAVLRGLALPTDCPLFGKTCTPRHPVGPCMVSYEGTCQIFYKYGVLF 372
                                    14        24        34   |    44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364        
                                                            38-CSD
   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  (0, 0)

(no "SCOP Domain" information available for 2Z1D)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2Z1D)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2Z1D)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A,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.

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        Q5JII1_THEKO | Q5JII1: 3vyr 3vys 3vyt 3vyu

(-) Related Entries Specified in the PDB File

2z1c 2z1e 2z1f