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(-) Description

Title :  CRYSTAL STRUCTURE OF NADP-DEPENDENT DEHYDROGENASE FROM RHODOBACTERSPHAEROIDES IN COMPLEX WITH NADP AND SULFATE
 
Authors :  M. Kowiel, O. A. Gasiorowska, I. G. Shabalin, K. B. Handing, P. J. Porebs J. Bonanno, S. C. Almo, W. Minor, New York Structural Genomics Res Consortium (Nysgrc)
Date :  08 May 15  (Deposition) - 20 May 15  (Release) - 20 May 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A (1x),B (1x)
Keywords :  2-Hydroxyacid Dehydrogenase, Nadp, Structural Genomics, Psi-Biology, New York Structural Genomics Research Consortium, Nysgrc (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Kowiel, O. A. Gasiorowska, I. G. Shabalin, K. B. Handing, P. J. Porebski, J. Bonanno, S. C. Almo, W. Minor
Crystal Structure Of Nadp-Dependent Dehydrogenase From Rhodobactersphaeroides In Complex With Nadp And Sulfate
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - NADP-DEPENDENT DEHYDROGENASE
    Chains: A, B
    EC Number: 1.1.1.79, 1.1.1.81
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PSGC-HIS
    Expression System Strain: BL21 (DE3) RIL
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: RSP_3442
    Organism Scientific: RHODOBACTER SPHAEROIDES (STRAIN ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158)
    Organism Taxid: 272943
    Strain: ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): AB
Biological Unit 2 (1x): A (1x)B (1x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 9)

Asymmetric Unit (5, 9)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2NAP2Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
3PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
4PGE1Ligand/IonTRIETHYLENE GLYCOL
5SO44Ligand/IonSULFATE ION
Biological Unit 1 (5, 9)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2NAP2Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
3PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
4PGE1Ligand/IonTRIETHYLENE GLYCOL
5SO44Ligand/IonSULFATE ION
Biological Unit 2 (4, 6)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2NAP1Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
3PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
4PGE-1Ligand/IonTRIETHYLENE GLYCOL
5SO43Ligand/IonSULFATE ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:90 , MET A:100 , GLY A:144 , LEU A:145 , GLY A:146 , GLU A:147 , LEU A:148 , TRP A:166 , SER A:167 , ARG A:168 , SER A:169 , LYS A:171 , LEU A:198 , LEU A:199 , PRO A:200 , THR A:205 , PHE A:226 , ALA A:227 , ARG A:228 , ASP A:252 , VAL A:253 , HIS A:276 , SER A:278 , ALA A:279 , TYR A:313 , SO4 A:402 , HOH A:517 , HOH A:527 , HOH A:548 , HOH A:552 , HOH A:556 , HOH A:557 , HOH A:560 , HOH A:562 , HOH A:574 , HOH A:614 , HOH A:682 , HOH A:721binding site for residue NAP A 401
2AC2SOFTWARETRP A:71 , GLY A:73 , ARG A:228 , HIS A:276 , NAP A:401 , HOH A:569 , HOH A:646 , HOH A:654binding site for residue SO4 A 402
3AC3SOFTWAREPRO A:62 , LEU A:64 , ARG A:86 , HOH A:530 , HOH A:543 , HOH A:601 , SER B:234 , PHE B:254 , GLU B:255 , LEU B:259 , SER B:263 , PRO B:264 , PHE B:265 , HOH B:510binding site for residue PGE A 403
4AC4SOFTWAREARG B:90 , MET B:100 , GLY B:144 , LEU B:145 , GLY B:146 , GLU B:147 , LEU B:148 , TRP B:166 , SER B:167 , ARG B:168 , SER B:169 , LYS B:171 , LEU B:198 , LEU B:199 , PRO B:200 , PHE B:226 , ALA B:227 , ARG B:228 , ASP B:252 , VAL B:253 , HIS B:276 , SER B:278 , ALA B:279 , ARG B:311 , TYR B:313 , SO4 B:402 , HOH B:515 , HOH B:520 , HOH B:528 , HOH B:531 , HOH B:580 , HOH B:581 , HOH B:586 , HOH B:593 , HOH B:614 , HOH B:660 , HOH B:703binding site for residue NAP B 401
5AC5SOFTWARETRP B:71 , ALA B:72 , GLY B:73 , ARG B:228 , HIS B:276 , NAP B:401 , HOH B:530 , HOH B:556 , HOH B:561 , HOH B:636 , HOH B:704binding site for residue SO4 B 402
6AC6SOFTWAREARG B:123 , THR B:300 , ARG B:302 , SO4 B:404 , HOH B:591 , HOH B:658 , HOH B:710binding site for residue SO4 B 403
7AC7SOFTWAREARG B:123 , ARG B:302 , SO4 B:403 , HOH B:603binding site for residue SO4 B 404
8AC8SOFTWAREGLU A:261 , ARG B:90 , SER B:306 , VAL B:307 , ASP B:308 , ARG B:311 , TYR B:313 , HOH B:581 , HOH B:638binding site for residue GOL B 405
9AC9SOFTWARETYR B:297 , GLY B:301binding site for residue PEG B 406

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4ZQB)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Glu A:257 -Pro A:258
2Glu B:257 -Pro B:258

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4ZQB)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4ZQB)

(-) Exons   (0, 0)

(no "Exon" information available for 4ZQB)

(-) 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:313
                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee..hhhhhhhhhhhhhhhh....eee.hhhhhhhhh.eeeeeee..hhhhhh......eeee....hhhhhhhhhhhh..ee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhh.eeeee....hhhhhhhhhhhh..eeeeee.........eeee...hhhhhhhhh.eeee............hhhhhhh....eeeee..hhhhhhhhhhhhhhhh..eeeeee....ee.............eee........hhhhhhhhhhhhhhhhhhhh............ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4zqb A   1 MSRIALVTRLSPEAEAHWAGHLARALPGERIDGFRELSPAERAEVDIAIVANPDPADLAELPNLVWIHSLWAGVERLVAELGHLARPIVRLVDPELARTMAEAALAWTYYLFRDMPAYAAQQRARVWKGLPYKRPERTTVGVLGLGELGAAAALRLRDAGFDVHGWSRSPKEIAGVTCHAGEETLERMLGQVEILVCLLPLTGETRGLLDARRLACLPEGAQIVNFARGPILDSAALIEALDSGRIGHAVLDVFEVEPLPEASPFWGHPKVTVLPHISAATDPETASAIVGAHVADYRATGRIPPSVDLTRGY 313
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310   


Chain B from PDB  Type:PROTEIN  Length:316
                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeee..hhhhhhhhhhhhhhhh....eee.hhhhhhhhh.eeeeeee..hhhhhh......eeee....hhhhhhhhhhhh..ee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhh.eeeee....hhhhhhhhhhhh..eeeeee....ee...eeee...hhhhhhh...eeee............hhhhhhh....eeeee..hhhhhhhhhhhhhhhh..eeeeee...................eee........hhhhhhhhhhhhhhhhhhhh............ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4zqb B  -2 FQSMSRIALVTRLSPEAEAHWAGHLARALPGERIDGFRELSPAERAEVDIAIVANPDPADLAELPNLVWIHSLWAGVERLVAELGHLARPIVRLVDPELARTMAEAALAWTYYLFRDMPAYAAQQRARVWKGLPYKRPERTTVGVLGLGELGAAAALRLRDAGFDVHGWSRSPKEIAGVTCHAGEETLERMLGQVEILVCLLPLTGETRGLLDARRLACLPEGAQIVNFARGPILDSAALIEALDSGRIGHAVLDVFEVEPLPEASPFWGHPKVTVLPHISAATDPETASAIVGAHVADYRATGRIPPSVDLTRGY 313
                                     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307
   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 4ZQB)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4ZQB)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4ZQB)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)

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