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(-) Description

Title :  CRYSTAL STRUCTURE OF NADPH-DEPENDENT GLYOXYLATE/HYDROXYPYRUVATE REDUCTASE SMC04462 (SMGHRB) FROM SINORHIZOBIUM MELILOTI IN APO FORM
 
Authors :  I. G. Shabalin, K. B. Handing, O. A. Gasiorowska, D. R. Cooper, J. Bonann S. C. Almo, W. Minor, New York Structural Genomics Research Cons (Nysgrc)
Date :  31 Jan 17  (Deposition) - 22 Feb 17  (Release) - 22 Feb 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Nadph-Dependent Glyoxylate/Hydroxypyruvate Reductase, Nadp, Nysgrc, Sinorhizobium Meliloti, Structural Genomics, Psi-Biology, New York Structural Genomics Research Consortium, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  I. G. Shabalin, K. B. Handing, W. Minor
Crystal Structure Of Nadph-Dependent Glyoxylate/Hydroxypyruvate Reductase From Sinorhizobium Meliloti In Complex With Citrate
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - NADPH-DEPENDENT GLYOXYLATE/HYDROXYPYRUVATE REDUCTASE
    Chains: A, B, C, D
    EC Number: 1.1.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PSGC-HIS
    Expression System Strain: BL21 (DE3) RIL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: SMC04462
    Organism Common: ENSIFER MELILOTI
    Organism Scientific: RHIZOBIUM MELILOTI (STRAIN 1021)
    Organism Taxid: 266834
    Strain: 1021

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 5)

Asymmetric Unit (1, 5)
No.NameCountTypeFull Name
1SO45Ligand/IonSULFATE ION
Biological Unit 1 (1, 3)
No.NameCountTypeFull Name
1SO43Ligand/IonSULFATE ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:172 , ARG A:173 , ARG A:176 , HOH A:557 , HOH A:583binding site for residue SO4 A 401
2AC2SOFTWAREARG A:230 , GLY A:231 , SER A:232 , HOH A:566 , HOH A:576binding site for residue SO4 A 402
3AC3SOFTWARETHR B:172 , ARG B:173 , ARG B:176binding site for residue SO4 B 401
4AC4SOFTWAREHIS C:184 , PRO C:185 , THR C:186 , GLY C:189binding site for residue SO4 C 401
5AC5SOFTWAREHIS D:184 , PRO D:185 , THR D:186 , GLY D:189 , MET D:190binding site for residue SO4 D 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5UOG)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Glu A:259 -Pro A:260
2Glu B:259 -Pro B:260
3Glu C:259 -Pro C:260
4Glu D:259 -Pro D:260

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5UOG)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5UOG)

(-) Exons   (0, 0)

(no "Exon" information available for 5UOG)

(-) 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:317
                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...hhhhhhhhhhh.eeeee...hhhhhhhhhh.eeeeee....hhhhhh......eeee........hhhhhhhh..eee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............eeeee.hhhhhhhhhhhhhhh..eeeee..........ee..hhhhhhhhh.eeee............hhhhhhhhh...eeee..hhhhhhhhhhhhhhhh....eeee.........hhhhhhh..eee.......hhhhhhhhhhhhhhhhhhhhhhh............... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5uog A   3 RPRILVPGKINPRVLERLPEMFETVRIERADAALVTADMRDVSGIAVSGKLPVPLMDAFPSLEIVANFGVGYDGVDVSRAAARGIVVTNTPDVLTEEVADTAIGLLLNTLRLLPQAEQWLRQGRWVREGAFPLSPLSLRGRTVGLFGLGRIGLAIARRLEAFGVSIAYHTRTPREGLGFTYHPTLVGMAEAVDTLIVIVPGTASTLKAVNADVLSALGPKGVLINVGRGSTVDEAALVTALQNGTIAGAGLDVFENEPNVPEALLSFPNVSLLPHVASASVVTRNAMSDLVVDNLKAWFSTGEALTPVAETPFRRRA 319
                                    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       


Chain B from PDB  Type:PROTEIN  Length:316
                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee...hhhhhhhhhhh.eeeee...hhhhhhhhhh.eeeeee....hhhhhh......eeee........hhhhhhhh..eee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............eeeee.hhhhhhhhhhhhhhh..eeeee..........ee..hhhhhhhhh.eeee..........hhhhhhhhh...eeee..hhhhhhhhhhhhhhhh....eeee.........hhhhhh...eee.......hhhhhhhhhhhhhhhhhhhhhhh............... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5uog B   2 SRPRILVPGKINPRVLERLPEMFETVRIERADAALVTADMRDVSGIAVSGKLPVPLMDAFPSLEIVANFGVGYDGVDVSRAAARGIVVTNTPDVLTEEVADTAIGLLLNTLRLLPQAEQWLRQGRWVREGAFPLSPLSLRGRTVGLFGLGRIGLAIARRLEAFGVSIAYHTRTPREGLGFTYHPTLVGMAEAVDTLIVIVPASTLKAVNADVLSALGPKGVLINVGRGSTVDEAALVTALQNGTIAGAGLDVFENEPNVPEALLSFPNVSLLPHVASASVVTRNAMSDLVVDNLKAWFSTGEALTPVAETPFRRRA 319
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201||     213       223       233       243       253       263       273       283       293       303       313      
                                                                                                                                                                                                                                  202|                                                                                                                  
                                                                                                                                                                                                                                   205                                                                                                                  


Chain C from PDB  Type:PROTEIN  Length:317
                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...hhhhhhhhhhh.eeeee...hhhhhhhhhh.eeeeee....hhhhhh......eeee........hhhhhhhh..eee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............eeeee.hhhhhhhhhhhhhhh..eeeee..........ee..hhhhhhhhh.eeee............hhhhhhhhh...eeee..hhhhhhhhhhhhhhhh....eeee.........hhhhhhh..eee.......hhhhhhhhhhhhhhhhhhhhhhh............... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5uog C   3 RPRILVPGKINPRVLERLPEMFETVRIERADAALVTADMRDVSGIAVSGKLPVPLMDAFPSLEIVANFGVGYDGVDVSRAAARGIVVTNTPDVLTEEVADTAIGLLLNTLRLLPQAEQWLRQGRWVREGAFPLSPLSLRGRTVGLFGLGRIGLAIARRLEAFGVSIAYHTRTPREGLGFTYHPTLVGMAEAVDTLIVIVPGTASTLKAVNADVLSALGPKGVLINVGRGSTVDEAALVTALQNGTIAGAGLDVFENEPNVPEALLSFPNVSLLPHVASASVVTRNAMSDLVVDNLKAWFSTGEALTPVAETPFRRRA 319
                                    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       


Chain D from PDB  Type:PROTEIN  Length:321
                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeee...hhhhhhhhhhh.eeeee...hhhhhhhhhh.eeeeee....hhhhhh......eeee........hhhhhhhh..eee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............eeeee.hhhhhhhhhhhhhhh..eeeee..........ee..hhhhhhhhh.eeee........hhhhhhhhh...eeee..hhhhhhhhhhhhhhhh....eeee.........hhhhhh...eee.......hhhhhhhhhhhhhhhhhhhhhhh............... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5uog D  -5 NLYFQSMSRPRILVPGKINPRVLERLPEMFETVRIERADAALVTADMRDVSGIAVSGKLPVPLMDAFPSLEIVANFGVGYDGVDVSRAAARGIVVTNTPDVLTEEVADTAIGLLLNTLRLLPQAEQWLRQGRWVREGAFPLSPLSLRGRTVGLFGLGRIGLAIARRLEAFGVSIAYHTRTPREGLGFTYHPTLVGMAEAVDTLIVIVSTLKAVNADVLSALGPKGVLINVGRGSTVDEAALVTALQNGTIAGAGLDVFENEPNVPEALLSFPNVSLLPHVASASVVTRNAMSDLVVDNLKAWFSTGEALTPVAETPFRRRA 319
                                     4        14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194      |208       218       228       238       248       258       268       278       288       298       308       318 
                                                                                                                                                                                                                                        201|                                                                                                                 
                                                                                                                                                                                                                                         206
   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 5UOG)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5UOG)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5UOG)

(-) Gene Ontology  (4, 4)

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        Q92LZ4_RHIME | Q92LZ4: 5j23 5v6q 5v72 5v7g 5v7n

(-) Related Entries Specified in the PDB File

5j23 COMPLEX WITH 2'-PHOSPHO-ADP-RIBOSE RELATED ID: NYSGRC-012132 RELATED DB: TARGETTRACK
5unn