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(-) Description

Title :  CRYSTAL STRUCTURE OF A PUTATIVE FORMATE DEHYDROGENASE FROM PYROBACULUM AEROPHILUM
 
Authors :  T. S. Peat, J. Newman, G. S. Waldo, T. C. Terwilliger
Date :  01 Jun 99  (Deposition) - 11 Jun 99  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Similar To The Previously Solved Formate Dehydrogenase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. S. Peat, J. Newman, G. S. Waldo, T. C. Terwilliger
The Crystal Structure Of A Putative Formate Dehydrogenase From Pyrobaculum Aerophilum
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - FORMATE DEHYDROGENASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector: T7 PROMOTER FROM A PET VECTOR
    Organism Scientific: PYROBACULUM AEROPHILUM
    Organism Taxid: 13773
    Other Details: FULL LENGTH PROTEIN WITH C-TERM HIS TAG (HHHHHH). HIS TAG WAS NOT SEEN IN THE DENSITY.
    Other Details - Source: HYPERTHERMOPHILIC ARCHEABACTERIUM

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 13)

Asymmetric/Biological Unit (2, 13)
No.NameCountTypeFull Name
1MSE12Mod. Amino AcidSELENOMETHIONINE
2NDP1Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:59 , GLY A:60 , ALA A:79 , ASN A:82 , LEU A:132 , GLY A:133 , GLU A:134 , ILE A:135 , SER A:154 , ARG A:155 , THR A:156 , PRO A:183 , ASN A:185 , HIS A:187 , THR A:188 , VAL A:209 , ARG A:211 , ASP A:235 , VAL A:236 , TRP A:260 , ALA A:262BINDING SITE FOR RESIDUE NDP A 310

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1QP8)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1QP8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1QP8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1QP8)

(-) Exons   (0, 0)

(no "Exon" information available for 1QP8)

(-) 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:302
 aligned with Q8ZXP5_PYRAE | Q8ZXP5 from UniProtKB/TrEMBL  Length:301

    Alignment length:302
                                                                                                                                                                                                                                                                                                                                      301 
                                    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| 
         Q8ZXP5_PYRAE     1 MELYVNFELPPEAEEELRKYFKIVRGGDLGNVEAALVSRITAEELAKMPRLKFIQVVTAGLDHLPWESIPPHVTVAGNAGSNADAVAEFALALLLAPYKRIIQYGEKMKRGDYGRDVEIPLIQGEKVAVLGLGEIGTRVGKILAALGAQVRGFSRTPKEGPWRFTNSLEEALREARAAVCALPLNKHTRGLVKYQHLALMAEDAVFVNVGRAEVLDRDGVLRILKERPQFIFASDVWWGRNDFAKDAEFFSLPNVVATPWVAGGYGNERVWRQMVMEAVRNLITYATGGRPRNIAKREDYI-   -
               SCOP domains d1qp8a2 A:1-82,A:264-302 Putative formate dehydrogenase                           d1qp8a1 A:83-263 Putative formate dehydrogenase                                                                                                                                      d1qp8a2 A:1-82,A:264-302                SCOP domains
               CATH domains -1qp8A01 A:2-82,A:264-302 NAD(P)-binding Rossmann-like Domain                     1qp8A02 A:83-263 NAD(P)-binding Rossmann-like Domain                                                                                                                                 1qp8A01 A:2-82,A:264-302                CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.....hhhhhhhhhh..eee................hhhhhhhh.....ee...................ee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...............eeeee...hhhhhhhhhhhhh..eeeee.......................eeee............hhhhhh......eeee..hhhh.hhhhhhhhhhhh...eeee........hhhhhhhhh...eee.........hhhhhhhhhhhhhhhhhhhhh........hhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qp8 A   1 mELYVNFELPPEAEEELRKYFKIVRGGDLGNVEAALVSRITAEELAKmPRLKFIQVVTAGLDHLPWESIPPHVTVAGNAGSNADAVAEFALALLLAPYKRIIQYGEKmKRGDYGRDVEIPLIQGEKVAVLGLGEIGTRVGKILAALGAQVRGFSRTPKEGPWRFTNSLEEALREARAAVCALPLNKHTRGLVKYQHLALmAEDAVFVNVGRAEVLDRDGVLRILKERPQFIFASDVWWGRNDFAKDAEFFSLPNVVATPWVAGGYGNERVWRQmVmEAVRNLITYATGGRPRNIAKREDYIG 302
                            |       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  
                            |                                             48-MSE                                                     108-MSE                                                                                     200-MSE                                                                   274-MSE                        
                            1-MSE                                                                                                                                                                                                                                                                            276-MSE                      


Chain B from PDB  Type:PROTEIN  Length:302
 aligned with Q8ZXP5_PYRAE | Q8ZXP5 from UniProtKB/TrEMBL  Length:301

    Alignment length:302
                                                                                                                                                                                                                                                                                                                                      301 
                                    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| 
         Q8ZXP5_PYRAE     1 MELYVNFELPPEAEEELRKYFKIVRGGDLGNVEAALVSRITAEELAKMPRLKFIQVVTAGLDHLPWESIPPHVTVAGNAGSNADAVAEFALALLLAPYKRIIQYGEKMKRGDYGRDVEIPLIQGEKVAVLGLGEIGTRVGKILAALGAQVRGFSRTPKEGPWRFTNSLEEALREARAAVCALPLNKHTRGLVKYQHLALMAEDAVFVNVGRAEVLDRDGVLRILKERPQFIFASDVWWGRNDFAKDAEFFSLPNVVATPWVAGGYGNERVWRQMVMEAVRNLITYATGGRPRNIAKREDYI-   -
               SCOP domains d1qp8b2 B:1-82,B:264-302 Putative formate dehydrogenase                           d1qp8b1 B:83-263 Putative formate dehydrogenase                                                                                                                                      d1qp8b2 B:1-82,B:264-302                SCOP domains
               CATH domains -1qp8B01 B:2-82,B:264-296 NAD(P)-binding Rossmann-like Domain                     1qp8B02 B:83-263 NAD(P)-binding Rossmann-like Domain                                                                                                                                 1qp8B01 B:2-82,B:264-296         ------ CATH domains
           Pfam domains (1) ------------------------2-Hacid_dh-1qp8B01 B:25-296                                                                                                                                                                                                                                                     ------ Pfam domains (1)
           Pfam domains (2) ------------------------2-Hacid_dh-1qp8B02 B:25-296                                                                                                                                                                                                                                                     ------ Pfam domains (2)
           Pfam domains (3) ------------------------------------------------------------------------------------------2-Hacid_dh_C-1qp8B03 B:91-262                                                                                                                                               ---------------------------------------- Pfam domains (3)
           Pfam domains (4) ------------------------------------------------------------------------------------------2-Hacid_dh_C-1qp8B04 B:91-262                                                                                                                                               ---------------------------------------- Pfam domains (4)
         Sec.struct. author .........hhhhhh.........................hhhhhhh..................................hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...............eeeee...hhhhhhhhhhhhh..eeeee.......................eeee............hhhhhh......eeee..hhhh.hhhhhhhhhhhh...eeee........hhhhhhhhh...eee.........hhhhhhhhhhhhhhhhhhh..........hhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qp8 B   1 mELYVNFELPPEAEEELRKYFKIVRGGDLGNVEAALVSRITAEELAKmPRLKFIQVVTAGLDHLPWESIPPHVTVAGNAGSNADAVAEFALALLLAPYKRIIQYGEKmKRGDYGRDVEIPLIQGEKVAVLGLGEIGTRVGKILAALGAQVRGFSRTPKEGPWRFTNSLEEALREARAAVCALPLNKHTRGLVKYQHLALmAEDAVFVNVGRAEVLDRDGVLRILKERPQFIFASDVWWGRNDFAKDAEFFSLPNVVATPWVAGGYGNERVWRQmVmEAVRNLITYATGGRPRNIAKREDYIG 302
                            |       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  
                            1-MSE                                         48-MSE                                                     108-MSE                                                                                     200-MSE                                                                   274-MSE                        
                                                                                                                                                                                                                                                                                                             276-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  (2, 4)

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

(-) CATH Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Clan: Form_Glyc_dh (56)
(-)
Clan: NADP_Rossmann (1239)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q8ZXP5_PYRAE | Q8ZXP5)
molecular function
    GO:0051287    NAD binding    Interacting selectively and non-covalently with nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NAD+, or the reduced form, NADH.
    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:0016616    oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor    Catalysis of an oxidation-reduction (redox) reaction in which a CH-OH group acts as a hydrogen or electron donor and reduces NAD+ or NADP.
    GO:0004617    phosphoglycerate dehydrogenase activity    Catalysis of the reaction: 3-phosphoglycerate + NAD+ = 3-phosphohydroxypyruvate + NADH + 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.
    GO:0009070    serine family amino acid biosynthetic process    The chemical reactions and pathways resulting in the formation of amino acids of the serine family, comprising cysteine, glycine, homoserine, selenocysteine and serine.

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