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(-) Description

Title :  ACINETOBACTER BAUMANNII RIBD, FORM 1
 
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 :  2.20
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Oxidoreductase, Reductase, Deaminase (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 - RIBOFLAVIN BIOSYNTHESIS PROTEIN RIBD
    Atcc: 19606
    Chains: A, B
    EC Number: 3.5.4.26, 1.1.1.193
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET15BTEV
    Expression System Vector Type: PLASMID
    Organism Scientific: ACINETOBACTER BAUMANNII
    Organism Taxid: 470
    Synonym: RIBD

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (3, 7)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2PO44Ligand/IonPHOSPHATE ION
3ZN2Ligand/IonZINC ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:54 , CYS A:79 , CYS A:88 , HOH A:2022BINDING SITE FOR RESIDUE ZN A 401
2AC2SOFTWAREHIS B:54 , CYS B:79 , CYS B:88 , HOH B:2016BINDING SITE FOR RESIDUE ZN B 401
3AC3SOFTWARELYS A:137 , LEU A:138 , ASN A:139 , GLN A:140 , GLY A:141 , ARG A:154 , ASP A:286BINDING SITE FOR RESIDUE ACT A 1359
4AC4SOFTWAREARG A:188 , CYS A:206 , GLN A:207 , LEU A:208 , ARG A:211 , HOH A:2074BINDING SITE FOR RESIDUE PO4 A 1360
5AC5SOFTWARELYS B:114 , ARG B:181 , ARG B:188 , CYS B:206 , GLN B:207 , LEU B:208 , ARG B:211BINDING SITE FOR RESIDUE PO4 B 1359
6AC6SOFTWAREASN A:28 , HIS A:54 , HIS A:81 , GLY A:83 , ARG A:84 , THR A:85 , HOH A:2013BINDING SITE FOR RESIDUE PO4 A 1361
7AC7SOFTWAREASN B:28 , HIS B:54 , GLY B:83 , ARG B:84 , THR B:85 , HOH B:2007 , HOH B:2008 , HOH B:2020BINDING SITE FOR RESIDUE PO4 B 1360

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Lys A:26 -Pro A:27
2Lys B:26 -Pro B:27

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3ZPC)

(-) 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:357
 aligned with D0CB74_ACIB2 | D0CB74 from UniProtKB/TrEMBL  Length:361

    Alignment length: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       
         D0CB74_ACIB2     2 SELKQDQYWMQQAIELAKRGLYSTKPNPNVGCVIVKDDQLIGEGFHPKAGQPHAEVFALRQAGEQAQGATAYVTLEPCAHYGRTPPCAEALVKAQVKKVVVACPDPNPLVAGKGVQILKNAGIEVEIGICEDLAAKLNQGFLKAMSTGMPYVRLKVASSLDGRTAMASGESKWITGSAARQDVQHWRAISGAVITGIDTVIADDCQLNVRSLHNIDIETVAQPKRVILDRRGRLPLTAKILENPETVMVMGPYRQELADLGVIQLEIQPLKTLLQTLSKQYQIYDVLIEAGATLSSAFLQEGLIDEMISYVAPTLLGQSARAMFNADFEYMAQQLRFKLLDVIQLDQDIRLRLIPTQ 358
               SCOP domains d3zpca1 A:2-150 automated matches                                                                                                                    d3zpca2 A:151-358 automated matches                                                                                                                                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhh.............eeeeee..eeeeeee.......hhhhhhhhhhhhhhh..eeeeee..........hhhhhhhhhh..eeeeee........hhhhhhhhhh..eeee..hhhhhhh.hhhhhhhhhhh..eeeeeeeee...eee..........hhhhhhhhhhhhhh..eeeeehhhhhhhh...........hhhhh...eeeee.........hhhhhhhh.eeee...hhhhhhhh.eee...hhhhhhhhhhhhhh..eeee..hhhhhhhhhhh....eeeeeee.ee.....ee.......hhhhheeeeeeeeeee..eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3zpc A   2 SELKQDQYWMQQAIELAKRGLYSTKPNPNVGCVIVKDDQLIGEGFHPKAGQPHAEVFALRQAGEQAQGATAYVTLEPCAHYGRTPPCAEALVKAQVKKVVVACPDPNPLVAGKGVQILKNAGIEVEIGICEDLAAKLNQGFLKAMSTGMPYVRLKVASSLDGRTAMASGESKWITGSAARQDVQHWRAISGAVITGIDTVIADDCQLNVRSLHNIDIETVAQPKRVILDRRGRLPLTAKILENPETVMVMGPYRQELADLGVIQLEIQPLKTLLQTLSKQYQIYDVLIEAGATLSSAFLQEGLIDEMISYVAPTLLGQSARAMFNADFEYMAQQLRFKLLDVIQLDQDIRLRLIPTQ 358
                                    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       


Chain B from PDB  Type:PROTEIN  Length:356
 aligned with D0CB74_ACIB2 | D0CB74 from UniProtKB/TrEMBL  Length:361

    Alignment length:356
                                    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       342       352      
         D0CB74_ACIB2     3 ELKQDQYWMQQAIELAKRGLYSTKPNPNVGCVIVKDDQLIGEGFHPKAGQPHAEVFALRQAGEQAQGATAYVTLEPCAHYGRTPPCAEALVKAQVKKVVVACPDPNPLVAGKGVQILKNAGIEVEIGICEDLAAKLNQGFLKAMSTGMPYVRLKVASSLDGRTAMASGESKWITGSAARQDVQHWRAISGAVITGIDTVIADDCQLNVRSLHNIDIETVAQPKRVILDRRGRLPLTAKILENPETVMVMGPYRQELADLGVIQLEIQPLKTLLQTLSKQYQIYDVLIEAGATLSSAFLQEGLIDEMISYVAPTLLGQSARAMFNADFEYMAQQLRFKLLDVIQLDQDIRLRLIPTQ 358
               SCOP domains d3zpcb1 B:3-150 automated matches                                                                                                                   d3zpcb2 B:151-358 automated matches                                                                                                                                                                              SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhh.........eeeee....eeeeee.......hhhhhhhhhhhhhhh..eeeeee..........hhhhhhhhh...eeeeee........hhhhhhhhhh..eeee..hhhhhhh.hhhhhhhhhhh..eeeeeeeee...eee..........hhhhhhhhhhhhhh..eeeeehhhhhhhh...........hhhhh...eeeee.........hhhhhhhh.eeee...hhhhhhhh.eee...hhhhhhhhhhhhhh..eeeee.hhhhhhhhhhh....eeeeeee.ee.....ee.......hhhhheeeeeeeeeee..eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3zpc B   3 ELKQDQYWMQQAIELAKRGLYSTKPNPNVGCVIVKDDQLIGEGFHPKAGQPHAEVFALRQAGEQAQGATAYVTLEPCAHYGRTPPCAEALVKAQVKKVVVACPDPNPLVAGKGVQILKNAGIEVEIGICEDLAAKLNQGFLKAMSTGMPYVRLKVASSLDGRTAMASGESKWITGSAARQDVQHWRAISGAVITGIDTVIADDCQLNVRSLHNIDIETVAQPKRVILDRRGRLPLTAKILENPETVMVMGPYRQELADLGVIQLEIQPLKTLLQTLSKQYQIYDVLIEAGATLSSAFLQEGLIDEMISYVAPTLLGQSARAMFNADFEYMAQQLRFKLLDVIQLDQDIRLRLIPTQ 358
                                    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       342       352
   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, 4)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (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

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

UniProtKB/TrEMBL
        D0CB74_ACIB2 | D0CB74: 3zpg

(-) Related Entries Specified in the PDB File

3zpg ACINETOBACTER BAUMANNII RIBD, FORM 2