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(-) Description

Title :  THE CRYSTAL STRUCTURE OF RIBD FROM ESCHERICHIA COLI IN COMPLEX WITH THE OXIDISED NADP+ COFACTOR IN THE ACTIVE SITE OF THE REDUCTASE DOMAIN
 
Authors :  M. Moche, P. Stenmark, D. Gurmu, P. Nordlund, Structural Proteomics (Spine)
Date :  11 Dec 06  (Deposition) - 13 Feb 07  (Release) - 03 Jun 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Nadp+ Complex, Alpha And Beta Class With Mainly Parallell Beta Strands, Structural Genomics, Htp-Protein Escherichia Coli, Structural Proteomics In Europe, Spine, Hydrolase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Stenmark, M. Moche, D. Gurmu, P. Nordlund
The Crystal Structure Of The Bifunctional Deaminase/Reductase Ribd Of The Riboflavin Biosynthetic Pathway In Escherichia Coli: Implications For The Reductive Mechanism.
J. Mol. Biol. V. 373 48 2007
PubMed-ID: 17765262  |  Reference-DOI: 10.1016/J.JMB.2006.12.009

(-) Compounds

Molecule 1 - RIBOFLAVIN BIOSYNTHESIS PROTEIN RIBD
    Chains: A, B
    EC Number: 3.5.4.26, 1.1.1.193
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PT73.3
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K12

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 19)

Asymmetric/Biological Unit (2, 19)
No.NameCountTypeFull Name
1MSE17Mod. Amino AcidSELENOMETHIONINE
2NAP2Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:152 , THR A:161 , ALA A:162 , MSE A:163 , ALA A:164 , TRP A:170 , SER A:193 , SER A:194 , ALA A:195 , THR A:196 , ASP A:200 , ASP A:233 , SER A:234 , ARG A:237 , HIS A:278 , LEU A:279 , LEU A:281 , ALA A:300 , GLY A:301 , PRO A:302 , THR A:303 , LEU A:304 , ALA A:307BINDING SITE FOR RESIDUE NAP A 402
2AC2SOFTWARELYS B:152 , TRP B:170 , SER B:193 , SER B:194 , ALA B:195 , THR B:196 , ASP B:200 , ILE B:232 , ASP B:233 , SER B:234 , ARG B:237 , HIS B:278 , LEU B:279 , LEU B:281 , GLU B:299 , ALA B:300 , GLY B:301 , PRO B:302 , THR B:303 , LEU B:304 , ALA B:307BINDING SITE FOR RESIDUE NAP B 1402

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:75 -A:85

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1His A:22 -Pro A:23
2Pro A:82 -Pro A:83
3His B:22 -Pro B:23

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2O7P)

(-) PROSITE Motifs  (2, 4)

Asymmetric/Biological Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CYT_DCMP_DEAMINASES_2PS51747 Cytidine and deoxycytidylate deaminases domain profile.RIBD_ECOLI1-123
 		  2A:2-123
B:2-123
2CYT_DCMP_DEAMINASES_1PS00903 Cytidine and deoxycytidylate deaminases zinc-binding region signature.RIBD_ECOLI50-88
 		  2A:50-88
B:50-88

(-) Exons   (0, 0)

(no "Exon" information available for 2O7P)

(-) 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:358
 aligned with Q3ZUB0_ECOLX | Q3ZUB0 from UniProtKB/TrEMBL  Length:367

    Alignment length:372
                                 1                                                                                                                                                                                                                                                                                                                                                                              
                                 |   5        15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365  
         Q3ZUB0_ECOLX     - -----MQDEYYMARALKLAQRGRFTTHPNPNVGCVIVKDGEIVGEGYHQRAGEPHAEVHALRMAGEKAKGATAYVTLEPCSHHGRTPPCCDALIAAGVARVVASMQDPNPQVAGRGLYRLQQAGIDVSHGLMMSEAEQLNKGFLKRMRTGFPYIQLKLGASLDGRTAMASGESQWITSPQARRDVQLLRAQSHAILTSSATVLADDPALTVRWSELDEQTQALYPQQNLRQPIRIVIDSQNRVTPVHRIVQQPGETWFARTQEDSREWPETVRTLLIPEHKGHLDLVVLMMQLGKQQINSIWVEAGPTLAGALLQAGLVDELIVYIAPKLLGSDARGLCTLPGLEKLADAPQFKFKEIRHVGPDVCLHLVGA 367
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhh.........eeeeee..eeeeeee.......hhhhhhhhhhhhhhh...eeeee...------.hhhhhhhhhh...eeeee....-....hhhhhhhhh...eee..hhhhhhhhhhhhhhhhhh...eeeeeeeee.........hhhhh..hhhhhhhhhhhhhh..eeeeehhhhhhhh.....hhhhh........hhhhh...eeeee.........hhhhh....eeeee...........eeeee..ee..eehhhhhhhhhhhh...eeee..hhhhhhhhhhhh...eeeeeee.................-------..eeeeeeee..eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2o7p A  -4 TLYIQGQDEYYmARALKLAQRGRFTTHPNPNVGCVIVKDGEIVGEGYHQRAGEPHAEVHALRmAGEKAKGATAYVTLEPC------PPCCDALIAAGVARVVASmQDPN-QVAGRGLYRLQQAGIDVSHGLmmSEAEQLNKGFLKRmRTGFPYIQLKLGASLDGRTAmASGESQWITSPQARRDVQLLRAQSHAILTSSATVLADDPALTVRWSELDEQTQALYPQQNLRQPIRIVIDSQNRVTPVHRIVQQPGETWFARTQEDSREWPETVRTLLIPEHKGHLDLVVLmmQLGKQQINSIWVEAGPTLAGALLQAGLVDELIVYIAPKLLGSDARGLCTLPGL-------QFKFKEIRHVGPDVCLHLVGA 367
                                     5 |      15        25        35        45        55  |     65        75      | 85        95    |   |-|      115       125 ||    135      |145       155       165       175       185       195       205       215       225       235       245       255       265       275       285|      295       305       315       325       335   |     - |     355       365  
                                       7-MSE                                             58-MSE           75     82               100-MSE |                  127-MSE        142-MSE              163-MSE                                                                                                                   285-MSE                                               339     347                    
                                                                                                                                        106                   128-MSE                                                                                                                                                       286-MSE                                                                             


Chain A from PDB  Type:PROTEIN  Length:358
 aligned with RIBD_ECOLI | P25539 from UniProtKB/Swiss-Prot  Length:367

    Alignment length:372
                                 1                                                                                                                                                                                                                                                                                                                                                                              
                                 |   5        15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365  
           RIBD_ECOLI     - -----MQDEYYMARALKLAQRGRFTTHPNPNVGCVIVKDGEIVGEGYHQRAGEPHAEVHALRMAGEKAKGATAYVTLEPCSHHGRTPPCCDALIAAGVARVVASMQDPNPQVAGRGLYRLQQAGIDVSHGLMMSEAEQLNKGFLKRMRTGFPYIQLKLGASLDGRTAMASGESQWITSPQARRDVQLLRAQSHAILTSSATVLADDPALTVRWSELDEQTQALYPQQNLRQPIRIVIDSQNRVTPVHRIVQQPGETWFARTQEDSREWPETVRTLLIPEHKGHLDLVVLMMQLGKQQINSIWVEAGPTLAGALLQAGLVDELIVYIAPKLLGSDARGLCTLPGLEKLADAPQFKFKEIRHVGPDVCLHLVGA 367
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhh.........eeeeee..eeeeeee.......hhhhhhhhhhhhhhh...eeeee...------.hhhhhhhhhh...eeeee....-....hhhhhhhhh...eee..hhhhhhhhhhhhhhhhhh...eeeeeeeee.........hhhhh..hhhhhhhhhhhhhh..eeeeehhhhhhhh.....hhhhh........hhhhh...eeeee.........hhhhh....eeeee...........eeeee..ee..eehhhhhhhhhhhh...eeee..hhhhhhhhhhhh...eeeeeee.................-------..eeeeeeee..eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) -----CYT_DCMP_DEAMINASES_2  PDB: A:2-123 UniProt: 1-123                                                                         ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) ------------------------------------------------------CYT_DCMP_DEAMINASES_1  PDB: A:50-88    --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2o7p A  -4 TLYIQGQDEYYmARALKLAQRGRFTTHPNPNVGCVIVKDGEIVGEGYHQRAGEPHAEVHALRmAGEKAKGATAYVTLEPC------PPCCDALIAAGVARVVASmQDPN-QVAGRGLYRLQQAGIDVSHGLmmSEAEQLNKGFLKRmRTGFPYIQLKLGASLDGRTAmASGESQWITSPQARRDVQLLRAQSHAILTSSATVLADDPALTVRWSELDEQTQALYPQQNLRQPIRIVIDSQNRVTPVHRIVQQPGETWFARTQEDSREWPETVRTLLIPEHKGHLDLVVLmmQLGKQQINSIWVEAGPTLAGALLQAGLVDELIVYIAPKLLGSDARGLCTLPGL-------QFKFKEIRHVGPDVCLHLVGA 367
                                     5 |      15        25        35        45        55  |     65        75      | 85        95    |   |-|      115       125 ||    135      |145       155       165       175       185       195       205       215       225       235       245       255       265       275       285|      295       305       315       325       335   |     - |     355       365  
                                       7-MSE                                             58-MSE           75     82               100-MSE |                  127-MSE        142-MSE              163-MSE                                                                                                                   285-MSE                                               339     347                    
                                                                                                                                        106                   128-MSE                                                                                                                                                       286-MSE                                                                             


Chain B from PDB  Type:PROTEIN  Length:353
 aligned with Q3ZUB0_ECOLX | Q3ZUB0 from UniProtKB/TrEMBL  Length:367

    Alignment length:372
                                 1                                                                                                                                                                                                                                                                                                                                                                              
                                 |   5        15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365  
         Q3ZUB0_ECOLX     - -----MQDEYYMARALKLAQRGRFTTHPNPNVGCVIVKDGEIVGEGYHQRAGEPHAEVHALRMAGEKAKGATAYVTLEPCSHHGRTPPCCDALIAAGVARVVASMQDPNPQVAGRGLYRLQQAGIDVSHGLMMSEAEQLNKGFLKRMRTGFPYIQLKLGASLDGRTAMASGESQWITSPQARRDVQLLRAQSHAILTSSATVLADDPALTVRWSELDEQTQALYPQQNLRQPIRIVIDSQNRVTPVHRIVQQPGETWFARTQEDSREWPETVRTLLIPEHKGHLDLVVLMMQLGKQQINSIWVEAGPTLAGALLQAGLVDELIVYIAPKLLGSDARGLCTLPGLEKLADAPQFKFKEIRHVGPDVCLHLVGA 367
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) ------dCMP_cyt_deam_1-2o7pB01 B:2-100                                                                    ---- -----------------------------------------RibD_C-2o7pB03         B:147-362                                                                                                                                                                                        ----- Pfam domains (1)
           Pfam domains (2) ------dCMP_cyt_deam_1-2o7pB02 B:2-100                                                                    ---- -----------------------------------------RibD_C-2o7pB04         B:147-362                                                                                                                                                                                        ----- Pfam domains (2)
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhh...........eeeeee..eeeeeee.......hhhhhhhhhhhhhhh...eee....----------.hhhhhhh...ee.......-......hhhhhhh........hhhhhhh.hhhhhhhhhh...eeeeeeeee.....--------...hhhhhhhhhhhhhhh.eeeeehhhhhhhh.....hhhhh.hhhhhh.hhhhh...eeeee.........hhhhh....eeeee...........eeeee..ee..eehhhhhhhhhhhh...eeee..hhhhhhhhhhh....eeeeeee................hhhhhh....eeeeeeee..eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2o7p B  -4 TLYIQGQDEYYmARALKLAQRGRFTTHPNPNVGCVIVKDGEIVGEGYHQRAGEPHAEVHALRmAGEKAKGATAYVTLEP----------CDALIAAGVARVVASmQDPN-QVAGRGLYRLQQAGIDVSHGLmmSEAEQLNKGFLKRmRTGFPYIQLKLGASLDGRT--------WITSPQARRDVQLLRAQSHAILTSSATVLADDPALTVRWSELDEQTQALYPQQNLRQPIRIVIDSQNRVTPVHRIVQQPGETWFARTQEDSREWPETVRTLLIPEHKGHLDLVVLmmQLGKQQINSIWVEAGPTLAGALLQAGLVDELIVYIAPKLLGSDARGLCTLPGLEKLADAPQFKFKEIRHVGPDVCLHLVGA 367
                                     5 |      15        25        35        45        55  |     65        |-        85        95    |   |-|      115       125 ||    135      |145       155     |   -    |  175       185       195       205       215       225       235       245       255       265       275       285|      295       305       315       325       335       345       355       365  
                                       7-MSE                                             58-MSE          74         85            100-MSE |                  127-MSE        142-MSE            161      170                                                                                                                285-MSE                                                                              
                                                                                                                                        106                   128-MSE                                                                                                                                                       286-MSE                                                                             


Chain B from PDB  Type:PROTEIN  Length:353
 aligned with RIBD_ECOLI | P25539 from UniProtKB/Swiss-Prot  Length:367

    Alignment length:372
                                 1                                                                                                                                                                                                                                                                                                                                                                              
                                 |   5        15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365  
           RIBD_ECOLI     - -----MQDEYYMARALKLAQRGRFTTHPNPNVGCVIVKDGEIVGEGYHQRAGEPHAEVHALRMAGEKAKGATAYVTLEPCSHHGRTPPCCDALIAAGVARVVASMQDPNPQVAGRGLYRLQQAGIDVSHGLMMSEAEQLNKGFLKRMRTGFPYIQLKLGASLDGRTAMASGESQWITSPQARRDVQLLRAQSHAILTSSATVLADDPALTVRWSELDEQTQALYPQQNLRQPIRIVIDSQNRVTPVHRIVQQPGETWFARTQEDSREWPETVRTLLIPEHKGHLDLVVLMMQLGKQQINSIWVEAGPTLAGALLQAGLVDELIVYIAPKLLGSDARGLCTLPGLEKLADAPQFKFKEIRHVGPDVCLHLVGA 367
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) ------dCMP_cyt_deam_1-2o7pB01 B:2-100                                                                    ---- -----------------------------------------RibD_C-2o7pB03         B:147-362                                                                                                                                                                                        ----- Pfam domains (1)
           Pfam domains (2) ------dCMP_cyt_deam_1-2o7pB02 B:2-100                                                                    ---- -----------------------------------------RibD_C-2o7pB04         B:147-362                                                                                                                                                                                        ----- Pfam domains (2)
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhh...........eeeeee..eeeeeee.......hhhhhhhhhhhhhhh...eee....----------.hhhhhhh...ee.......-......hhhhhhh........hhhhhhh.hhhhhhhhhh...eeeeeeeee.....--------...hhhhhhhhhhhhhhh.eeeeehhhhhhhh.....hhhhh.hhhhhh.hhhhh...eeeee.........hhhhh....eeeee...........eeeee..ee..eehhhhhhhhhhhh...eeee..hhhhhhhhhhh....eeeeeee................hhhhhh....eeeeeeee..eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) -----CYT_DCMP_DEAMINASES_2  PDB: B:2-123 UniProt: 1-123                                                                         ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) ------------------------------------------------------CYT_DCMP_DEAMINASES_1  PDB: B:50-88    --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2o7p B  -4 TLYIQGQDEYYmARALKLAQRGRFTTHPNPNVGCVIVKDGEIVGEGYHQRAGEPHAEVHALRmAGEKAKGATAYVTLEP----------CDALIAAGVARVVASmQDPN-QVAGRGLYRLQQAGIDVSHGLmmSEAEQLNKGFLKRmRTGFPYIQLKLGASLDGRT--------WITSPQARRDVQLLRAQSHAILTSSATVLADDPALTVRWSELDEQTQALYPQQNLRQPIRIVIDSQNRVTPVHRIVQQPGETWFARTQEDSREWPETVRTLLIPEHKGHLDLVVLmmQLGKQQINSIWVEAGPTLAGALLQAGLVDELIVYIAPKLLGSDARGLCTLPGLEKLADAPQFKFKEIRHVGPDVCLHLVGA 367
                                     5 |      15        25        35        45        55  |     65        |-        85        95    |   |-|      115       125 ||    135      |145       155     |   -    |  175       185       195       205       215       225       235       245       255       265       275       285|      295       305       315       325       335       345       355       365  
                                       7-MSE                                             58-MSE          74         85            100-MSE |                  127-MSE        142-MSE            161      170                                                                                                                285-MSE                                                                              
                                                                                                                                        106                   128-MSE                                                                                                                                                       286-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  (0, 0)

(no "SCOP Domain" information available for 2O7P)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2O7P)

(-) Pfam Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Clan: CDA (39)
(-)
Clan: DHFred (95)

(-) Gene Ontology  (14, 24)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (RIBD_ECOLI | P25539)
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: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:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    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).
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

Chain A,B   (Q3ZUB0_ECOLX | Q3ZUB0)
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: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: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 Specified in the PDB File

2g6v THE CRYSTAL STRUCTURE OF APO RIBD FROM ESCHERICHIA COLI
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