2P4G - JenaLib

Title :   CRYSTAL STRUCTURE OF A PYRIMIDINE REDUCTASE-LIKE PROTEIN (DIP1392) FROM CORYNEBACTERIUM DIPHTHERIAE NCTC AT 2.30 A RESOLUTION

Authors :   Joint Center For Structural Genomics (Jcsg)

Date :   12 Mar 07 (Deposition) - 27 Mar 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

Chains :   Asym. Unit : A
Biol. Unit 1: A  (2x)

Keywords :   Pyrimidine Reductase-Like Protein, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Hypothetical Protein (Np_939744. 1) Fro Corynebacterium Diphtheriae At 2. 30 A Resolution
To Be Published
PubMed: search

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 18)

Sites (16, 16)

Asymmetric Unit (16, 16)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	MSE A:56 , GLY A:57 , ARG A:239 , ASN A:250 , HOH A:329	BINDING SITE FOR RESIDUE NO3 A 270
02	AC2	SOFTWARE	GLU A:85 , TYR A:87 , EDO A:275	BINDING SITE FOR RESIDUE EDO A 271
03	AC3	SOFTWARE	GLY A:78 , THR A:81 , GLY A:195 , PRO A:196 , SER A:197 , VAL A:198 , EDO A:282	BINDING SITE FOR RESIDUE EDO A 272
04	AC4	SOFTWARE	PRO A:89 , SER A:124 , GLU A:125 , HOH A:353 , HOH A:378 , HOH A:386	BINDING SITE FOR RESIDUE EDO A 273
05	AC5	SOFTWARE	GLU A:243 , LEU A:245 , SER A:247 , HOH A:371	BINDING SITE FOR RESIDUE EDO A 274
06	AC6	SOFTWARE	ARG A:69 , TYR A:87 , GLY A:88 , PRO A:89 , EDO A:271	BINDING SITE FOR RESIDUE EDO A 275
07	AC7	SOFTWARE	ALA A:79 , ARG A:83 , PHE A:120 , HOH A:294 , HOH A:359 , HOH A:368	BINDING SITE FOR RESIDUE EDO A 276
08	AC8	SOFTWARE	CYS A:106 , LEU A:108 , PRO A:109 , LYS A:110 , GLU A:134	BINDING SITE FOR RESIDUE EDO A 277
09	AC9	SOFTWARE	ILE A:38 , ILE A:40 , ASP A:61 , GLU A:193 , EDO A:280 , HOH A:351	BINDING SITE FOR RESIDUE EDO A 278
10	BC1	SOFTWARE	TYR A:22 , GLY A:70 , ARG A:100 , ARG A:105	BINDING SITE FOR RESIDUE EDO A 279
11	BC2	SOFTWARE	ALA A:39 , ILE A:40 , SER A:53 , GLY A:195 , PRO A:196 , TYR A:199 , EDO A:278	BINDING SITE FOR RESIDUE EDO A 280
12	BC3	SOFTWARE	LEU A:118 , TYR A:119 , PHE A:120 , PHE A:122 , GLU A:125 , LYS A:157 , HOH A:307 , HOH A:361 , HOH A:372	BINDING SITE FOR RESIDUE EDO A 281
13	BC4	SOFTWARE	GLY A:78 , ALA A:79 , GLU A:80 , LEU A:114 , SER A:115 , LYS A:116 , EDO A:272 , HOH A:334	BINDING SITE FOR RESIDUE EDO A 282
14	BC5	SOFTWARE	SER A:117 , ASP A:130 , PRO A:144 , SER A:148	BINDING SITE FOR RESIDUE EDO A 283
15	BC6	SOFTWARE	SER A:53 , THR A:81 , GLU A:85	BINDING SITE FOR RESIDUE EDO A 284
16	BC7	SOFTWARE	SER A:133 , SER A:136 , GLY A:162 , HOH A:308	BINDING SITE FOR RESIDUE EDO A 285

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
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	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
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Chain A from PDB  Type:PROTEIN  Length:248
 aligned with Q6NGV8_CORDI | Q6NGV8 from UniProtKB/TrEMBL  Length:269

    Alignment length:248
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254        
         Q6NGV8_CORDI    15 VTTEQIVYGALPLTTINEPECRAIAITSINGSATLSGVSGPMGDQTDADLLIQLRGWADAIVVGAETARKENYGPVVLPHGIKNQRQKLGRCGLPKLTLLSKSLYFDFSSELFSPDLPSELSPLVITQQPANNSEQWDQRLQKLIDVGVEVIVAPTSTNPLKIAFDALHARRLKKISIEGGPSVYRQALSLGIVDRLHLTIAPNIICPVESPLFGKISDDSFTTRLVLEMLSSSPNGLIFSRYKVIRD 262
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2p4gA00 A:15-262 Dihydrofolate Reductase, subunit A                                                                                                                                                                                                      CATH domains
               Pfam domains ---------------------RibD_C-2p4gA01 A:36-254                                                                                                                                                                                                    -------- Pfam domains
         Sec.struct. author .hhhhhhhh...hhhhhh.eeeeeeeee..........hhhhhhhhhhhhhhhhhhhh.eeeeehhhhhhh.......hhhhhhhhhhh......eeeee.........hhhhh...hhhhh.eeeee.....hhhhhhhhhhhhhhh..eeee....hhhhhhhhhhhh....eeeeeehhhhhhhhhhhh...eeeeeee.......................eeeeeeee.....eeeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2p4g A  15 VTTEQIVYGALPLTTINEPECRAIAITSINGSATLSGVSGPmGDQTDADLLIQLRGWADAIVVGAETARKENYGPVVLPHGIKNQRQKLGRCGLPKLTLLSKSLYFDFSSELFSPDLPSELSPLVITQQPANNSEQWDQRLQKLIDVGVEVIVAPTSTNPLKIAFDALHARRLKKISIEGGPSVYRQALSLGIVDRLHLTIAPNIICPVESPLFGKISDDSFTTRLVLEmLSSSPNGLIFSRYKVIRD 262
                                    24        34        44        54 |      64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254        
                                                                    56-MSE                                                                                                                                                                                     244-MSE

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	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (1, 1)

Pfam Domains (1, 1)

Gene Ontology (3, 3)

Asymmetric Unit(hide GO term definitions)

Chain A (Q6NGV8_CORDI | Q6NGV8)

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.
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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