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(-) Description

Title :  CRYSTAL STRUCTURE OF HYDROGENASE MATURATION PROTEIN HYPE IN COMPLEX WITH ATP
 
Authors :  Y. Shomura, Y. Higuchi
Date :  15 May 07  (Deposition) - 09 Oct 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Alpha-Beta Fold, Beta Barrel, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Shomura, H. Komori, N. Miyabe, M. Tomiyama, N. Shibata, Y. Higuchi
Crystal Structures Of Hydrogenase Maturation Protein Hype I The Apo And Atp-Bound Forms
J. Mol. Biol. V. 372 1045 2007
PubMed-ID: 17706667  |  Reference-DOI: 10.1016/J.JMB.2007.07.023

(-) Compounds

Molecule 1 - HYDROGENASE EXPRESSION/FORMATION PROTEIN HYPE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PPROEXHTB
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: HYPE
    Organism Scientific: DESULFOVIBRIO VULGARIS SUBSP. VULGARIS
    Organism Taxid: 882
    Strain: HILDENBOROUGH

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
1ATP1Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2MG2Ligand/IonMAGNESIUM ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1ATP2Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:54 , ASP A:127 , ATP A:342 , HOH A:453BINDING SITE FOR RESIDUE MG A 343
2AC2SOFTWAREASP A:39 , ASP A:79 , ASP A:218 , ATP A:342 , HOH A:434BINDING SITE FOR RESIDUE MG A 344
3AC3SOFTWAREILE A:21 , PHE A:25 , LEU A:34 , LEU A:37 , ASN A:38 , ASP A:39 , ASP A:54 , ASP A:79 , CYS A:92 , PHE A:94 , THR A:125 , GLY A:126 , ASP A:127 , THR A:128 , LYS A:129 , THR A:220 , ARG A:221 , MG A:343 , MG A:344 , HOH A:354 , HOH A:370 , HOH A:371 , HOH A:372 , HOH A:405 , HOH A:434 , HOH A:453 , HOH A:512BINDING SITE FOR RESIDUE ATP A 342

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2Z1U)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Asp A:59 -Pro A:60
2Asp A:152 -Pro A:153
3Leu A:309 -Gly A:310

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2Z1U)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2Z1U)

(-) Exons   (0, 0)

(no "Exon" information available for 2Z1U)

(-) 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:335
 aligned with Q72F88_DESVH | Q72F88 from UniProtKB/TrEMBL  Length:341

    Alignment length:337
                                    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       
         Q72F88_DESVH     5 TLLLDYGSGGRASHRLISDLFLRHFDNPILGTLNDAARLDLTGPLAMSTDSYTVDPIFFPGGDIGTLAVHGTVNDVSMLGARPRYLSCGFILEEGLDMDILERVVASMGKAAREAGVFIVTGDTKVVPRGACDKMFINTTGIGEILVDPAPSGDRARPGDAILISGSMGDHGLTILSQRQGLNFAADVCSDSASLNRVVEKLVLEVGDIHVLRDPTRGGLATTLNEIAGQSQAVCHVLETAVPVRESVRNGCSFLGLDPLYLANEGKLICILPEERAEAALAVLREGPHGEHAARIGSVKSVGELGAARAGQVVMETALGGHRLLSMLEGEQLPRIC 341
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------AIRS-2z1uA01 A:37-128                                                                       --------------------------------AIRS_C-2z1uA02 A:161-312                                                                                                                                ----------------------------- Pfam domains
         Sec.struct. author ..hhhhhh.hhhhhhhhhhhhhhhhhhhhhhh............eeeeeeee.....ee..eehhhhhhhhhhhhhhh..eeeeeeeeeeeee...hhhhhhhhhhhhhhhhhhhh.eeeeeeeeee.......eeeeeeeeeee......hhhhh....eeee....hhhhhhhhhhh...............hhhhhhhhhhhh....eee....hhhhhhhhhhhhhhh.eeeee.hhh..hhhhhhhhhhh.............eeeehhhhhhhhhhhhhh..hhhhheeeeeee............eeee.....eee.....--...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2z1u A   5 TLLLDYGSGGRASHRLISDLFLRHFDNPILGTLNDAARLDLTGPLAMSTDSYTVDPIFFPGGDIGTLAVHGTVNDVSMLGARPRYLSCGFILEEGLDMDILERVVASMGKAAREAGVFIVTGDTKVVPRGACDKMFINTTGIGEILVDPAPSGDRARPGDAILISGSMGDHGLTILSQRQGLNFAADVCSDSASLNRVVEKLVLEVGDIHVLRDPTRGGLATTLNEIAGQSQAVCHVLETAVPVRESVRNGCSFLGLDPLYLANEGKLICILPEERAEAALAVLREGPHGEHAARIGSVKSVGELGAARAGQVVMETALGGHRLLSMLE--QLPRIC 341
                                    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        |- |     
                                                                                                                                                                                                                                                                                                                                                                  333  |     
                                                                                                                                                                                                                                                                                                                                                                     336
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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 2Z1U)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2Z1U)

(-) Pfam Domains  (2, 2)

Asymmetric Unit
(-)
Clan: no clan defined [family: AIRS] (11)
(-)
Clan: no clan defined [family: AIRS_C] (13)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q72F88_DESVH | Q72F88)
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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  2z1u
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 Related Entries

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

UniProtKB/TrEMBL
        Q72F88_DESVH | Q72F88: 2z1t

(-) Related Entries Specified in the PDB File

2z1t