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(-) Description

Title :  CRYSTAL STRUCTURE OF AMIDOHYDROLASE DR_0824 FROM DEINOCOCCUS RADIODURANS
 
Authors :  S. Eswaramoorthy, S. K. Burley, S. Swaminathan, New York Sgx Research Center For Structural Genomics (Nysgxrc)
Date :  04 Oct 06  (Deposition) - 17 Oct 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.78
Chains :  Asym./Biol. Unit :  A
Keywords :  Zinc, Nysgxrc, Psi2, 9256A, Structural Genomics, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Eswaramoorthy, S. K. Burley, S. Swaminathan
Crystal Structure Of A Hypothetical Protein Dr_0824 From Deinococcus Radiodurans
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HYPOTHETICAL PROTEIN DR_0824
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: DEINOCOCCUS RADIODURANS
    Organism Taxid: 1299

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1ZN1Ligand/IonZINC ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:97 , HIS A:99 , HIS A:238 , ASP A:352 , HOH A:554BINDING SITE FOR RESIDUE ZN A 500

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Ser A:53 -Pro A:54

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2IMR)

(-) Sequences/Alignments

Asymmetric/Biological 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:380
 aligned with MQNX_DEIRA | Q9RW45 from UniProtKB/Swiss-Prot  Length:418

    Alignment length:385
                                    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       373       383       393       403       413     
           MQNX_DEIRA    34 HTPRLLTCDVLYTGMGGAQSPGGVVVVGETVAAAGHPDELRRQYPHAAEERAGAVIAPPPVNAHTHLDMSAYEFQALPYFQWIPEVVIRGRHLRGVAAAQAGADTLTRLGAGGVGDIVWAPEVMDALLAREDLSGTLYFEVLNPFPDKADEVFAAARTHLERWRRLERPGLRLGLSPHTPFTVSHRLMRLLSDYAAGEGLPLQIHVAEHPTELEMFRTGGGPLWDNRMPALYPHTLAEVIGREPGPDLTPVRYLDELGVLAARPTLVHMVNVTPDDIARVARAGCAVVTCPRSNHHLECGTFDWPAFAAAGVEVALGTDSVASGETLNVREEVTFARQLYPGLDPRVLVRAAVKGGQRVVGGRTPFLRRGETWQEGFRWELSRDL 418
               SCOP domains d2imra1 A:34-   90,A:399-418 Hypothetical protein DR0824 d2imra2 A:91-398 Hypothetical protein DR0824                                                                                                                                                                                                                                                                        d2imra1              SCOP domains
               CATH domains 2imrA01     2   i2imrA01 A:34-45,A:51-90,A:400-416       2imrA02 A:46-50,A:91-399 Metal-dependent hydrolases                                                                                                                                                                                                                                                                  2imrA01          -- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.ee..---.....eeeeee..eeeeeehhhhhhhhh...eeee...ee.....eeeee...hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh....eeeee.hhhhhhhhhh.....eeeeeee...hhhhhhhhhhhhhhhhhhhhh.....eeeeeee......hhhhhhhhhhhhhhhh...eeee..hhhhhhhhhhh...hhhhhhhhhh..hhhhhhh.......hhhhhhhhh.hhhhh.eeee....hhhhhhhhhhhh..eeehhhhhhhh.....hhhhhhhh...eee...hhhhhh...hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh--..........hhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2imr A  34 HTPRLLTCDVLYT---GAQSPGGVVVVGETVAAAGHPDELRRQYPHAAEERAGAVIAPPPVNAHTHLDMSAYEFQALPYFQWIPEVVIRGRHLRGVAAAQAGADTLTRLGAGGVGDIVWAPEVMDALLAREDLSGTLYFEVLNPFPDKADEVFAAARTHLERWRRLERPGLRLGLSPHTPFTVSHRLMRLLSDYAAGEGLPLQIHVAEHPTELEMFRTGGGPLWDNRMPALYPHTLAEVIGREPGPDLTPVRYLDELGVLAARPTLVHMVNVTPDDIARVARAGCAVVTCPRSNHHLECGTFDWPAFAAAGVEVALGTDSVASGETLNVREEVTFARQLYPGLDPRVLVRAAVKGGQRVVG--TPFLRRGETWQEGFRWELSRDL 418
                                    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       373       383       393|  |   403       413     
                                       46  50                                                                                                                                                                                                                                                                                                                                                     394  |                     
                                                                                                                                                                                                                                                                                                                                                                                                     397
   Legend:   → Mismatch (orange background)
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  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  (2, 2)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (MQNX_DEIRA | Q9RW45)
molecular function
    GO:0019239    deaminase activity    Catalysis of the removal of an amino group from a substrate, producing ammonia (NH3).
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0016810    hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds    Catalysis of the hydrolysis of any carbon-nitrogen bond, C-N, with the exception of peptide bonds.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0009234    menaquinone biosynthetic process    The chemical reactions and pathways resulting in the formation of any of the menaquinones. Structurally, menaquinones consist of a methylated naphthoquinone ring structure and side chains composed of a variable number of unsaturated isoprenoid residues. Menaquinones that have vitamin K activity and are known as vitamin K2.

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