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(-) Description

Title :  ACINETOBACTER BAUMANNII RIBD, FORM 2
 
Authors :  A. Dawson, P. Trumper, G. Chrysostomou, W. N. Hunter
Date :  27 Feb 13  (Deposition) - 27 Mar 13  (Release) - 28 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.99
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Reductase, Deaminase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Dawson, P. Trumper, G. Chrysostomou, W. N. Hunter
Structure Of Diaminohydroxyphosphoribosylaminopyrimidine Deaminase/5-Amino-6-(5-Phosphoribosylamino)Uracil Reductase From Acinetobacter Baumannii.
Acta Crystallogr. , Sect. F V. 69 611 2013
PubMed-ID: 23722836  |  Reference-DOI: 10.1107/S174430911301292X

(-) Compounds

Molecule 1 - RIBD
    Atcc: 19606
    Chains: A
    EC Number: 3.5.4.26, 1.1.1.193
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15BTEV
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: ACINETOBACTER BAUMANNII
    Organism Taxid: 470

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (7, 10)

Asymmetric Unit (7, 10)
No.NameCountTypeFull Name
15GP2Ligand/IonGUANOSINE-5'-MONOPHOSPHATE
2ACT1Ligand/IonACETATE ION
3CAC1Ligand/IonCACODYLATE ION
4CL1Ligand/IonCHLORIDE ION
5OXL2Ligand/IonOXALATE ION
6SO42Ligand/IonSULFATE ION
7ZN1Ligand/IonZINC ION
Biological Unit 1 (5, 16)
No.NameCountTypeFull Name
15GP4Ligand/IonGUANOSINE-5'-MONOPHOSPHATE
2ACT2Ligand/IonACETATE ION
3CAC2Ligand/IonCACODYLATE ION
4CL-1Ligand/IonCHLORIDE ION
5OXL4Ligand/IonOXALATE ION
6SO44Ligand/IonSULFATE ION
7ZN-1Ligand/IonZINC ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:54 , CYS A:79 , CYS A:88 , CAC A:1364BINDING SITE FOR RESIDUE ZN A 1358
02AC2SOFTWAREARG A:188 , CYS A:206 , GLN A:207 , LEU A:208 , ARG A:211BINDING SITE FOR RESIDUE SO4 A 1359
03AC3SOFTWAREHIS A:54 , GLY A:83 , ARG A:84 , THR A:85BINDING SITE FOR RESIDUE SO4 A 1360
04AC4SOFTWARELEU A:229 , ARG A:231 , MET A:251 , PRO A:270 , LEU A:271 , ALA A:298 , GLU A:302 , HOH A:2087 , HOH A:2101 , HOH A:2102 , HOH A:2123 , HOH A:2124 , HOH A:2125BINDING SITE FOR RESIDUE 5GP A 1361
05AC5SOFTWAREPHE A:46 , PRO A:48 , PHE A:58 , HOH A:2126BINDING SITE FOR RESIDUE OXL A 1362
06AC6SOFTWAREILE A:198 , LEU A:229 , ARG A:231 , ARG A:232 , ARG A:234 , HOH A:2088BINDING SITE FOR RESIDUE OXL A 1363
07AC7SOFTWAREHIS A:54 , GLU A:56 , LEU A:76 , GLU A:77 , PRO A:78 , CYS A:79 , CYS A:88 , ZN A:1358 , HOH A:2023BINDING SITE FOR RESIDUE CAC A 1364
08AC8SOFTWAREGLY A:197 , THR A:200 , GLY A:292 , HOH A:2107BINDING SITE FOR RESIDUE CL A 1365
09AC9SOFTWARELYS A:137 , LEU A:138 , ASN A:139 , GLN A:140 , ARG A:154 , ASP A:286BINDING SITE FOR RESIDUE ACT A 1366
10BC1SOFTWARELYS A:137 , ASP A:183 , HIS A:186 , ARG A:351 , ARG A:353 , HOH A:2127BINDING SITE FOR RESIDUE 5GP A 1367

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3ZPG)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Lys A:26 -Pro A:27

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3ZPG)

(-) 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:354
 aligned with D0CB74_ACIB2 | D0CB74 from UniProtKB/TrEMBL  Length:361

    Alignment length:356
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351      
         D0CB74_ACIB2     2 SELKQDQYWMQQAIELAKRGLYSTKPNPNVGCVIVKDDQLIGEGFHPKAGQPHAEVFALRQAGEQAQGATAYVTLEPCAHYGRTPPCAEALVKAQVKKVVVACPDPNPLVAGKGVQILKNAGIEVEIGICEDLAAKLNQGFLKAMSTGMPYVRLKVASSLDGRTAMASGESKWITGSAARQDVQHWRAISGAVITGIDTVIADDCQLNVRSLHNIDIETVAQPKRVILDRRGRLPLTAKILENPETVMVMGPYRQELADLGVIQLEIQPLKTLLQTLSKQYQIYDVLIEAGATLSSAFLQEGLIDEMISYVAPTLLGQSARAMFNADFEYMAQQLRFKLLDVIQLDQDIRLRLIPT 357
               SCOP domains d3zpga1 A:2-150 automated matches                                                                                                                    d3zpga2 A:151-357 auto  mated matches                                                                                                                                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhh.........eeeeee..eeeeeee.......hhhhhhhhhhhhhhh..eeeeee..........hhhhhhhhh...eeeeee........hhhhhhhhhh..eeee..hhhhhhh.hhhhhhhhhhh..eeeeeeeee............--..hhhhhhhhhhhhhh..eeeeehhhhhhhh...........hhhhh...eeeee.........hhhhhhhh.eeee...hhhhhhh..eee...hhhhhhhhhhhhhh..eeeee.hhhhhhhhhhh....eeeeeee.................hhhhh..eeeeeeeee..eeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3zpg A   2 SELKQDQYWMQQAIELAKRGLYSTKPNPNVGCVIVKDDQLIGEGFHPKAGQPHAEVFALRQAGEQAQGATAYVTLEPCAHYGRTPPCAEALVKAQVKKVVVACPDPNPLVAGKGVQILKNAGIEVEIGICEDLAAKLNQGFLKAMSTGMPYVRLKVASSLDGRTAMASGES--ITGSAARQDVQHWRAISGAVITGIDTVIADDCQLNVRSLHNIDIETVAQPKRVILDRRGRLPLTAKILENPETVMVMGPYRQELADLGVIQLEIQPLKTLLQTLSKQYQIYDVLIEAGATLSSAFLQEGLIDEMISYVAPTLLGQSARAMFNADFEYMAQQLRFKLLDVIQLDQDIRLRLIPT 357
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171|  |   181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351      
                                                                                                                                                                                                    172  |                                                                                                                                                                                      
                                                                                                                                                                                                       175
   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  (2, 2)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A   (D0CB74_ACIB2 | D0CB74)
molecular function
    GO:0008703    5-amino-6-(5-phosphoribosylamino)uracil reductase activity    Catalysis of the reaction: 5-amino-6-(5-phosphoribitylamino)uracil + NADP(+) = 5-amino-6-(5-phosphoribosylamino)uracil + H(+) + NADPH.
    GO:0050661    NADP binding    Interacting selectively and non-covalently with nicotinamide-adenine dinucleotide phosphate, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NADP+, or the reduced form, NADPH.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0008835    diaminohydroxyphosphoribosylaminopyrimidine deaminase activity    Catalysis of the reaction: 2,5-diamino-6-hydroxy-4-(5-phosphoribosylamino)-pyrimidine + H(2)O + H(+) = 5-amino-6-(5-phosphoribosylamino)uracil + NH(4)(+).
    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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
    GO:0009231    riboflavin biosynthetic process    The chemical reactions and pathways resulting in the formation of riboflavin (vitamin B2), the precursor for the coenzymes flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD).

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 Related Entries

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        D0CB74_ACIB2 | D0CB74: 3zpc

(-) Related Entries Specified in the PDB File

3zpc ACINETOBACTER BAUMANNII RIBD, FORM 1