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(-) Description

Title :  THE CRYSTAL STRUCTURE OF OXIDOREDUCTASE FROM MARINOBACTER AQUAEOLEI
 
Authors :  Z. Zhang, S. C. Almo, S. Swaminathan, New York Structural Genomics Consortium (Nysgrc)
Date :  11 Apr 11  (Deposition) - 04 May 11  (Release) - 04 May 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.63
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Structural Genomics, Psi-Biology, New York Structural Genomics Research Consortium, Nysgrc, Oxidoreductase, Abm20716. 1 (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Z. Zhang, S. C. Almo, S. Swaminathan
The Crystal Structure Of Oxidoreductase From Marinobacter Aquaeolei
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - SUCCINATE-SEMIALDEHYDE DEHYDROGENASE (NAD(P)(+))
    Chains: A, B
    EC Number: 1.2.1.16
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET
    Expression System Strain: BL21 (DE3) RIP
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: MAQU_3647
    Organism Scientific: MARINOBACTER AQUAEOLEI
    Organism Taxid: 351348
    Strain: VT8

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 28)

Asymmetric/Biological Unit (1, 28)
No.NameCountTypeFull Name
1MSE28Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 3RH9)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3RH9)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3RH9)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3RH9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3RH9)

(-) Exons   (0, 0)

(no "Exon" information available for 3RH9)

(-) 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:481
 aligned with A1U6U7_MARHV | A1U6U7 from UniProtKB/TrEMBL  Length:482

    Alignment length:481
                                    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       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480 
         A1U6U7_MARHV     1 MIESPLLENLTGYIGGRWKDSAGGATFDVYNPATGSVIAKVPSMPEEDVVAAVEAGQSALRLTNPWPIETRRKWLEDIRDGLKENREEIGRILCMEHGKPWKEAQGEVDYAAGFFDYCAKHISALDSHTIPEKPKDCTWTVHYRPVGVTGLIVPWNFPIGMIAKKLSAALAAGCPSVIKPASETPLTMIAFFSVMDKLDLPDGMVNLVMGKASVIGKVLCEHKDVPMLSFTGSTEVGRKLIVDTAEQVKKLALELGGNAPFIVFDDADLEAAADNLIANKFRGGGQTCVCANRIFVHEKVADAFGQKLAERVNKMTVGDGMNDGIDIGPLINKQGFDKVKRHLQDALDKGASLVAGKQPAELGDGLFFPPTVVQGVDREMCCYQEETFGPLVPMALFRTEEEVIDAGNDTEFGLASYVFTADAERAQRVAAGLRFGHVGWNTGTGPTPEAPFGGMKASGIGREGGLEGLFEFVEAQTVPRG 481
               SCOP domains d3rh9a_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhh...eee..eee......eeeee......eeeeee..hhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh.ee...hhhhheeeeeeee...eeee......hhhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhh........eee...hhhhhhhhhhhh....eeeee.hhhhhhhhhhhh.....eeeee.....eeee....hhhhhhhhhhhhhhhhhhh......eeeee..hhhhhhhhhhhhhhhh................hhhhhhhhhhhhhhhhhh..eeee..hhhhh........eeee.....hhhhhh.....eeeeeee.hhhhhhhhhh......eeeee..hhhhhhhhhhhh...eeee..............hhh.ee...hhhhhhh..eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3rh9 A   1 mIESPLLENLTGYIGGRWKDSAGGATFDVYNPATGSVIAKVPSmPEEDVVAAVEAGQSALRLTNPWPIETRRKWLEDIRDGLKENREEIGRILCmEHGKPWKEAQGEVDYAAGFFDYCAKHISALDSHTIPEKPKDCTWTVHYRPVGVTGLIVPWNFPIGmIAKKLSAALAAGCPSVIKPASETPLTmIAFFSVmDKLDLPDGmVNLVmGKASVIGKVLCEHKDVPmLSFTGSTEVGRKLIVDTAEQVKKLALELGGNAPFIVFDDADLEAAADNLIANKFRGGGQTCVCANRIFVHEKVADAFGQKLAERVNKmTVGDGmNDGIDIGPLINKQGFDKVKRHLQDALDKGASLVAGKQPAELGDGLFFPPTVVQGVDREmCCYQEETFGPLVPmALFRTEEEVIDAGNDTEFGLASYVFTADAERAQRVAAGLRFGHVGWNTGTGPTPEAPFGGmKASGIGREGGLEGLFEFVEAQTVPRG 481
                            |       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    |  320|      330       340       350       360       370       380       390   |   400       410       420       430       440       450    |  460       470       480 
                            |                                         44-MSE                                             95-MSE                                                           161-MSE                    188-MSE  |      204-MSE|               227-MSE                                                                                 315-MSE |                                                        380-MSE       394-MSE                                                      455-MSE                      
                            1-MSE                                                                                                                                                                                           195-MSE       209-MSE                                                                                                         321-MSE                                                                                                                                                            


Chain B from PDB  Type:PROTEIN  Length:476
 aligned with A1U6U7_MARHV | A1U6U7 from UniProtKB/TrEMBL  Length:482

    Alignment length:480
                                    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       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480
         A1U6U7_MARHV     1 MIESPLLENLTGYIGGRWKDSAGGATFDVYNPATGSVIAKVPSMPEEDVVAAVEAGQSALRLTNPWPIETRRKWLEDIRDGLKENREEIGRILCMEHGKPWKEAQGEVDYAAGFFDYCAKHISALDSHTIPEKPKDCTWTVHYRPVGVTGLIVPWNFPIGMIAKKLSAALAAGCPSVIKPASETPLTMIAFFSVMDKLDLPDGMVNLVMGKASVIGKVLCEHKDVPMLSFTGSTEVGRKLIVDTAEQVKKLALELGGNAPFIVFDDADLEAAADNLIANKFRGGGQTCVCANRIFVHEKVADAFGQKLAERVNKMTVGDGMNDGIDIGPLINKQGFDKVKRHLQDALDKGASLVAGKQPAELGDGLFFPPTVVQGVDREMCCYQEETFGPLVPMALFRTEEEVIDAGNDTEFGLASYVFTADAERAQRVAAGLRFGHVGWNTGTGPTPEAPFGGMKASGIGREGGLEGLFEFVEAQTVPR 480
               SCOP domains d3rh9b_ B: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhh.................eeeee......eeeeee..hhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh.ee...hhhhheeeeeeee...eeee......hhhhhhhhhhhhhh...eeee.....hhhhhhhhhhhh........eee...hhhhhhhhhhhh....eeeee.hhhhhhhhhhhh.....eeeee.....eeee....hhhhhhhhhhhhhhhhhhh......eeeee..hhhhhhhhhhhhhh..................hhhhhhhhhhhhhhhhhh..eeee..hhhhh----....eeeeee...hhhhhh.....eeeeeee.hhhhhhhhhh......eeeee..hhhhhhhhhhhh...eeee..............hhh.ee...hhhhhhh..eeeeeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3rh9 B   1 mIESPLLENLTGYIGGRWKDSAGGATFDVYNPATGSVIAKVPSmPEEDVVAAVEAGQSALRLTNPWPIETRRKWLEDIRDGLKENREEIGRILCmEHGKPWKEAQGEVDYAAGFFDYCAKHISALDSHTIPEKPKDCTWTVHYRPVGVTGLIVPWNFPIGmIAKKLSAALAAGCPSVIKPASETPLTmIAFFSVmDKLDLPDGmVNLVmGKASVIGKVLCEHKDVPmLSFTGSTEVGRKLIVDTAEQVKKLALELGGNAPFIVFDDADLEAAADNLIANKFRGGGQTCVCANRIFVHEKVADAFGQKLAERVNKmTVGDGmNDGIDIGPLINKQGFDKVKRHLQDALDKGASLVAGKQPAEL----FFPPTVVQGVDREmCCYQEETFGPLVPmALFRTEEEVIDAGNDTEFGLASYVFTADAERAQRVAAGLRFGHVGWNTGTGPTPEAPFGGmKASGIGREGGLEGLFEFVEAQTVPR 480
                            |       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    |  320|      330       340       350       360 |    |370       380       390   |   400       410       420       430       440       450    |  460       470       480
                            1-MSE                                     44-MSE                                             95-MSE                                                           161-MSE                    188-MSE  |      204-MSE|               227-MSE                                                                                 315-MSE |                                      362  367          380-MSE       394-MSE                                                      455-MSE                     
                                                                                                                                                                                                                            195-MSE       209-MSE                                                                                                         321-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  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3RH9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3RH9)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (A1U6U7_MARHV | A1U6U7)
molecular function
    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:0016620    oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor    Catalysis of an oxidation-reduction (redox) reaction in which an aldehyde or ketone (oxo) group acts as a hydrogen or electron donor and reduces NAD or NADP.
    GO:0009013    succinate-semialdehyde dehydrogenase [NAD(P)+] activity    Catalysis of the reaction: succinate semialdehyde + NAD(P)+ + H2O = succinate + NAD(P)H + H+.
biological process
    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.

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