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(-) Description

Title :  CRYSTAL STRUCTURE OF A DIAMINOHYDROXYPHOSPHORIBOSYLAMINOPYRIMIDINE DEAMINASE/ 5-AMINO-6-(5-PHOSPHORIBOSYLAMINO)URACIL REDUCTASE (TM1828) FROM THERMOTOGA MARITIMA AT 1.80 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  04 Aug 06  (Deposition) - 15 Aug 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Oxidoreductase, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Biosynthetic Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Diaminohydroxyphosphoribosylaminopyrimidine Deaminase/ 5-Amino-6-(5-Phosphoribosylamino)Uracil Reductase (Tm1828) From Thermotoga Maritima At 1. 80 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - DIAMINOHYDROXYPHOSPHORIBOSYLAMINOPYRIMIDINE DEAMINASE/ 5- AMINO-6-(5-PHOSPHORIBOSYLAMINO)URACIL REDUCTASE
    Chains: A
    EC Number: 3.5.4.26, 1.1.1.193
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: TM1828
    Organism Scientific: THERMOTOGA MARITIMA
    Organism Taxid: 2336

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 16)

Asymmetric Unit (5, 16)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2GOL8Ligand/IonGLYCEROL
3MSE5Mod. Amino AcidSELENOMETHIONINE
4NDP1Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
5ZN1Ligand/IonZINC ION
Biological Unit 1 (3, 28)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GOL16Ligand/IonGLYCEROL
3MSE10Mod. Amino AcidSELENOMETHIONINE
4NDP2Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
5ZN-1Ligand/IonZINC ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:49 , CYS A:77 , CYS A:86 , HOH A:708BINDING SITE FOR RESIDUE ZN A 500
02AC2SOFTWAREARG A:184 , LEU A:204 , GOL A:505 , HOH A:596 , HOH A:714BINDING SITE FOR RESIDUE CL A 501
03AC3SOFTWAREALA A:155 , ILE A:162 , GLY A:167 , SER A:169 , GLY A:193 , ALA A:194 , GLY A:195 , THR A:196 , LYS A:199 , ASP A:200 , LEU A:219 , ASP A:220 , ARG A:221 , LYS A:222 , CYS A:261 , ILE A:266 , GLU A:281 , GLY A:283 , SER A:284 , LYS A:285 , VAL A:286 , GLU A:289 , LEU A:310 , GOL A:503 , HOH A:524 , HOH A:527 , HOH A:605BINDING SITE FOR RESIDUE NDP A 400
04AC4SOFTWAREARG A:19 , GLY A:67 , GLY A:94 , ASN A:185 , GLU A:210 , GLY A:211 , HOH A:526BINDING SITE FOR RESIDUE GOL A 502
05AC5SOFTWARESER A:169 , ILE A:172 , THR A:173 , NDP A:400 , GOL A:505 , HOH A:606 , HOH A:704BINDING SITE FOR RESIDUE GOL A 503
06AC6SOFTWAREARG A:147 , ASP A:292 , ASP A:295BINDING SITE FOR RESIDUE GOL A 504
07AC7SOFTWAREASP A:200 , GLU A:281 , CL A:501 , GOL A:503BINDING SITE FOR RESIDUE GOL A 505
08AC8SOFTWAREVAL A:31 , LYS A:32 , ASP A:33 , GLY A:34 , GLY A:67 , ALA A:68 , THR A:69BINDING SITE FOR RESIDUE GOL A 506
09AC9SOFTWARETHR A:303 , LYS A:304 , ILE A:305 , TYR A:316 , PRO A:323 , PRO A:324 , LYS A:325 , HOH A:539BINDING SITE FOR RESIDUE GOL A 507
10BC1SOFTWARELYS A:179 , ASN A:330 , GLU A:332 , GLU A:341BINDING SITE FOR RESIDUE GOL A 508
11BC2SOFTWAREASP A:88 , GLU A:92 , HIS A:119 , LYS A:209BINDING SITE FOR RESIDUE GOL A 509

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Asn A:21 -Pro A:22
2Gly A:282 -Gly A:283

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2HXV)

(-) 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:349
 aligned with Q9X2E8_THEMA | Q9X2E8 from UniProtKB/TrEMBL  Length:348

    Alignment length:349
                                1                                                                                                                                                                                                                                                                                                                                                         
                                |    6        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         
         Q9X2E8_THEMA     - ----MYETFMKRAIELAKKGLGRVNPNPPVGAVVVKDGRIIAEGFHPYFGGPHAERMAIESARKKGEDLRGATLIVTLEPCDHHGKTPPCTDLIIESGIKTVVIGTRDPNPVSGNGVEKFRNHGIEVIEGVLEEEVKKLCEFFITYVTKKRPFVALKYASTLDGKIADHRGDSKWITDKLRFKVHEMRNIYSAVLVGAGTVLKDNPQLTCRLKEGRNPVRVILDRKGVLSGKVFRVFEENARVIVFTESEEAEYPPHVEKALSDCSVESILRNLYERDIDSVLVEGGSKVFSEFLDHADVVFGFYSTKIFGKGLDVFSGYLSDVSVPPKFKVVNVEFSDSEFLVEMRPC 345
               SCOP domains ----d2hxva2 A:1-147 Riboflavin biosynthesis protein RibD                                                                                               d2hxva1 A:148-345 Riboflavin biosynthesis protein RibD                                                                                                                                                 SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------2hxvA02 A:148-345 Dihydrofolate Reductase, subunit A                                                                                                                                                   CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhh...........eeeeee..eeeeeee.......hhhhhhhhhhhhh.......eeeeee..........hhhhhhhhhh..eeeeee...hhhhhhhhhhhhh...eeee..hhhhhhhhhhhhhhhhhhh..eeeeeeeee...eee............hhhhhhhhhhhh.eeeeehhhhhhhh.............eeeee..........hhhhh....eeeee...........eeee...hhhhhhhhhhhh...eeee..hhhhhhhhhhhh.eeeeeee.......ee..............eeeeeeeee..eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2hxv A  -3 HHHHmYETFmKRAIELAKKGLGRVNPNPPVGAVVVKDGRIIAEGFHPYFGGPHAERmAIESARKKGEDLRGATLIVTLEPCDHHGKTPPCTDLIIESGIKTVVIGTRDPNPVSGNGVEKFRNHGIEVIEGVLEEEVKKLCEFFITYVTKKRPFVALKYASTLDGKIADHRGDSKWITDKLRFKVHEmRNIYSAVLVGAGTVLKDNPQLTCRLKEGRNPVRVILDRKGVLSGKVFRVFEENARVIVFTESEEAEYPPHVEKALSDCSVESILRNLYERDIDSVLVEGGSKVFSEFLDHADVVFGFYSTKIFGKGLDVFSGYLSDVSVPPKFKVVNVEFSDSEFLVEmRPC 345
                                |    6        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     |   
                                |    |                                             53-MSE                                                                                                                           183-MSE                                                                                                                                                        342-MSE
                                1-MSE|                                                                                                                                                                                                                                                                                                                                                   
                                     6-MSE
   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  (1, 1)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q9X2E8_THEMA | Q9X2E8)
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: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:0019239    deaminase activity    Catalysis of the removal of an amino group from a substrate, producing ammonia (NH3).
    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: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.
    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:0009451    RNA modification    The covalent alteration of one or more nucleotides within an RNA molecule to produce an RNA molecule with a sequence that differs from that coded genetically.
    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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