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(-) Description

Title :  CRYSTAL STRUCTURE OF ADP/ATP-DEPENDENT NAD(P)H-HYDRATE DEHYDRATASE FROM BACILLUS SUBTILIS CO-CRYSTALLIZED WITH ATP/MG2+ AND SOAKED WITH NADPH
 
Authors :  I. A. Shumilin, M. Cymborowski, A. Joachimiak, W. Minor, Midwest Cent Structural Genomics (Mcsg)
Date :  27 Apr 11  (Deposition) - 27 Jul 11  (Release) - 09 Jan 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.51
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (4x)
Keywords :  Structural Genomics, Psi-Biology, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Lyase, Lyase-Lyase Substrate Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  I. A. Shumilin, M. Cymborowski, O. Chertihin, K. N. Jha, J. C. Herr, S. A. Lesley, A. Joachimiak, W. Minor
Identification Of Unknown Protein Function Using Metabolite Cocktail Screening.
Structure V. 20 1715 2012
PubMed-ID: 22940582  |  Reference-DOI: 10.1016/J.STR.2012.07.016

(-) Compounds

Molecule 1 - ADP/ATP-DEPENDENT NAD(P)H-HYDRATE DEHYDRATASE
    Chains: A
    EC Number: 4.2.1.93
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG19
    Expression System Strain: BL21-CODONPLUS (DE3)-RIPL
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: BSU38720, YXKO
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (4x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 3)

Asymmetric Unit (3, 3)
No.NameCountTypeFull Name
1AMP1Ligand/IonADENOSINE MONOPHOSPHATE
2MG1Ligand/IonMAGNESIUM ION
3NPW1Ligand/IonBETA-6-HYDROXY-1,4,5,6-TETRAHYDRONICOTINAMIDE ADENINEDINUCLEOTIDE PHOSPHATE
Biological Unit 1 (2, 8)
No.NameCountTypeFull Name
1AMP4Ligand/IonADENOSINE MONOPHOSPHATE
2MG-1Ligand/IonMAGNESIUM ION
3NPW4Ligand/IonBETA-6-HYDROXY-1,4,5,6-TETRAHYDRONICOTINAMIDE ADENINEDINUCLEOTIDE PHOSPHATE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:186 , AMP A:278 , HOH A:297 , HOH A:303 , HOH A:306 , HOH A:322BINDING SITE FOR RESIDUE MG A 277
2AC2SOFTWAREALA A:20 , SER A:22 , LYS A:24 , HIS A:149 , LYS A:186 , GLY A:187 , THR A:190 , ASN A:206 , GLY A:207 , LEU A:209 , ALA A:210 , THR A:214 , GLY A:215 , LEU A:218 , HIS A:243 , MG A:277 , HOH A:285 , HOH A:295 , HOH A:303 , HOH A:317 , HOH A:322 , HOH A:340 , HOH A:345 , HOH A:388BINDING SITE FOR RESIDUE AMP A 278
3AC3SOFTWAREHIS A:23 , LYS A:24 , GLY A:25 , MET A:39 , ALA A:42 , LYS A:57 , PRO A:75 , GLU A:76 , ALA A:77 , THR A:78 , PRO A:103 , GLY A:104 , ALA A:129 , HIS A:149 , PRO A:150 , GLY A:151 , VAL A:161 , GLY A:213 , ASP A:216 , HOH A:280 , HOH A:291 , HOH A:301 , HOH A:306 , HOH A:317 , HOH A:322 , HOH A:323 , HOH A:365 , HOH A:388 , HOH A:424 , HOH A:438 , HOH A:439 , HOH A:444 , HOH A:446 , HOH A:508 , HOH A:512BINDING SITE FOR RESIDUE NPW A 279

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (3, 3)

Asymmetric Unit (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1YJEF_C_3PS51383 YjeF C-terminal domain profile.NNRD_BACSU7-275  1A:7-275
2YJEF_C_1PS01049 YjeF C-terminal domain signature 1.NNRD_BACSU98-108  1A:98-108
3YJEF_C_2PS01050 YjeF C-terminal domain signature 2.NNRD_BACSU212-222  1A:212-222
Biological Unit 1 (3, 12)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1YJEF_C_3PS51383 YjeF C-terminal domain profile.NNRD_BACSU7-275  4A:7-275
2YJEF_C_1PS01049 YjeF C-terminal domain signature 1.NNRD_BACSU98-108  4A:98-108
3YJEF_C_2PS01050 YjeF C-terminal domain signature 2.NNRD_BACSU212-222  4A:212-222

(-) Exons   (0, 0)

(no "Exon" information available for 3RPZ)

(-) 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:277
 aligned with NNRD_BACSU | P94368 from UniProtKB/Swiss-Prot  Length:276

    Alignment length:277
                             1                                                                                                                                                                                                                                                                                   
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       
           NNRD_BACSU     - -MNVPFWTEEHVRATLPERDAESHKGTYGTALLLAGSDDMPGAALLAGLGAMRSGLGKLVIGTSENVIPLIVPVLPEATYWRDGWKKAADAQLEETYRAIAIGPGLPQTESVQQAVDHVLTADCPVILDAGALAKRTYPKREGPVILTPHPGEFFRMTGVPVNELQKKRAEYAKEWAAQLQTVIVLKGNQTVIAFPDGDCWLNPTGNGALAKGGTGDTLTGMILGMLCCHEDPKHAVLNAVYLHGACAELWTDEHSAHTLLAHELSDILPRVWKRFE 276
               SCOP domains d3rpza_ A: automated matches                                                                                                                                                                                                                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhh.......hhhhh.eeeee......hhhhhhhhhhhhh....eeeeee...hhhhhh......eeeehhhhhh..........eeee......hhhhhhhhhhhh.....eee.hhhh...........eee..hhhhhhhhhh.hhhhhh.hhhhhhhhhhhhhh.eeee.....eee.....eee....hhhhh..hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -------YJEF_C_3  PDB: A:7-275 UniProt: 7-275                                                                                                                                                                                                                                        - PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------------------------YJEF_C_1   -------------------------------------------------------------------------------------------------------YJEF_C_2   ------------------------------------------------------ PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3rpz A   0 AMNVPFWTEEHVRATLPERDAESHKGTYGTALLLAGSDDMPGAALLAGLGAMRSGLGKLVIGTSENVIPLIVPVLPEATYWRDGWKKAADAQLEETYRAIAIGPGLPQTESVQQAVDHVLTADCPVILDAGALAKRTYPKREGPVILTPHPGEFFRMTGVPVNELQKKRAEYAKEWAAQLQTVIVLKGNQTVIAFPDGDCWLNPTGNGALAKGGTGDTLTGMILGMLCCHEDPKHAVLNAVYLHGACAELWTDEHSAHTLLAHELSDILPRVWKRFE 276
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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, 1)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A   (NNRD_BACSU | P94368)
molecular function
    GO:0052855    ADP-dependent NAD(P)H-hydrate dehydratase activity    Catalysis of the reaction: (6S)-6beta-hydroxy-1,4,5,6-tetrahydronicotinamide adenine dinucleotide + ADP = AMP + 3 H(+) + NADH + phosphate.
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
    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.
biological process
    GO:0046496    nicotinamide nucleotide metabolic process    The chemical reactions and pathways involving nicotinamide nucleotides, any nucleotide that contains combined nicotinamide.

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  3rpz
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  NNRD_BACSU | P94368
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  4.2.1.93
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        NNRD_BACSU | P94368: 1kyh 3rph 3rq2 3rq5 3rq6 3rq8 3rqh 3rqq 3rqx

(-) Related Entries Specified in the PDB File

1kyh APO-PROTEIN
3rq5 CRYSTAL STRUCTURE OF ADP/ATP-DEPENDENT NAD(P)H-HYDRATE DEHYDRATASE FROM BACILLUS SUBTILIS CO-CRYSTALLIZED WITH ATP/MG2+ AND SOAKED WITH COA
3rq6 CRYSTAL STRUCTURE OF ADP/ATP-DEPENDENT NAD(P)H-HYDRATE DEHYDRATASE FROM BACILLUS SUBTILIS SOAKED WITH ADP-RIBOSE
3rq8 CRYSTAL STRUCTURE OF ADP/ATP-DEPENDENT NAD(P)H-HYDRATE DEHYDRATASE FROM BACILLUS SUBTILIS SOAKED WITH P1,P5- DI(ADENOSINE-5') PENTAPHOSPHATE
3rqh CRYSTAL STRUCTURE OF ADP/ATP-DEPENDENT NAD(P)H-HYDRATE DEHYDRATASE FROM BACILLUS SUBTILIS IN COMPLEX WITH P1,P6- DI(ADENOSINE-5') HEXAPHOSPHATE
3rqq CRYSTAL STRUCTURE OF ADP/ATP-DEPENDENT NAD(P)H-HYDRATE DEHYDRATASE FROM BACILLUS SUBTILIS IN COMPLEX WITH P1,P3- DI(ADENOSINE-5') TRIPHOSPHATE
3rqx CRYSTAL STRUCTURE OF ADP/ATP-DEPENDENT NAD(P)H-HYDRATE DEHYDRATASE FROM BACILLUS SUBTILIS IN COMPLEX WITH P1,P4- DI(ADENOSINE-5') TETRAPHOSPHATE