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(-) Description

Title :  CRYSTAL STRUCTURE OF A PUTATIVE SERINE HYDROLASE (YDR428C) FROM SACCHAROMYCES CEREVISIAE AT 1.85 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  20 May 04  (Deposition) - 08 Jun 04  (Release) - 13 Jul 11  (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 :  Putative Serine Hydrolase, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. W. Arndt, R. Schwarzenbacher, R. Page, P. Abdubek, E. Ambing, T. Biorac, J. M. Canaves, H. J. Chiu, X. Dai, A. M. Deacon, M. Didonato, M. A. Elsliger, A. Godzik, C. Grittini, S. K. Grzechnik, J. Hale, E. Hampton, G. W. Han, J. Haugen, M. Hornsby, H. E. Klock, E. Koesema, A. Kreusch, P. Kuhn, L. Jaroszewski, S. A. Lesley, I. Levin, D. Mcmullan, T. M. Mcphillips, M. D. Miller, A. Morse, K. Moy, E. Nigoghossian, J. Ouyang, W. S. Peti, K. Quijano, R. Reyes, E. Sims, G. Spraggon, R. C. Stevens, H. Van Den Bedem, J. Velasquez, J. Vincent, F. Von Delft, X. Wang, B. West, A. White, G. Wolf, Q. Xu, O. Zagnitko, K. O. Hodgson, J. Wooley, I. A. Wilson
Crystal Structure Of An Alpha/Beta Serine Hydrolase (Ydr428C) From Saccharomyces Cerevisiae At 1. 85 A Resolutio
Proteins V. 58 755 2005
PubMed-ID: 15624212  |  Reference-DOI: 10.1002/PROT.20336

(-) Compounds

Molecule 1 - PUTATIVE SERINE HYDROLASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: YDR428C
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932

 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  (3, 18)

Asymmetric Unit (3, 18)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2GOL2Ligand/IonGLYCEROL
3MSE15Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (2, 17)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GOL2Ligand/IonGLYCEROL
3MSE15Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (2, 10)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GOL2Ligand/IonGLYCEROL
3MSE8Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:131 , GLU A:132 , ALA A:133 , SER B:131 , GLU B:132 , ALA B:133 , HOH B:547BINDING SITE FOR RESIDUE CL B 455
2AC2SOFTWARETHR A:28 , ARG A:29 , GLU A:30 , GLY A:100 , THR A:102 , ASN A:103BINDING SITE FOR RESIDUE GOL A 456
3AC3SOFTWAREASP A:228 , HOH A:673BINDING SITE FOR RESIDUE GOL A 457

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (5, 5)

Asymmetric Unit
No.Residues
1Ser A:9 -Pro A:10
2Ser A:76 -Pro A:77
3Asn A:81 -Pro A:82
4Ser B:76 -Pro B:77
5Asn B:81 -Pro B:82

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (1, 2)

Asymmetric Unit (1, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YDR428C1YDR428C.1IV:1324232-1323447786KFA_YEAST1-2612612A:-1-261
B:10-261		261
252

(-) 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:261
 aligned with KFA_YEAST | Q04066 from UniProtKB/Swiss-Prot  Length:261

    Alignment length:261
                                    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 
            KFA_YEAST     1 MSNTVRAISPDITLFNKTLTFQEISQNTREAVIYIHGGAWNDPENTPNDFNQLANTIKSMDTESTVCQYSIEYRLSPEITNPRNLYDAVSNITRLVKEKGLTNINMVGHSVGATFIWQILAALKDPQEKMSEAQLQMLGLLQIVKRVFLLDGIYSLKELLVEYPEYDCFTRLAFPDGIQMYEEEPSRVMPYVKKALSRFSIDMHLVHSYSDELLTLRQTNCLISCLQDYQLSFKLYLDDLGLHNDVYKNGKVAKYIFDNIC 261
               SCOP domains d1vkha_ A: Putative serine hydrolase Ydr428c                                                                                                                                                                                                                          SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............hhhhheeee.......eeeeee..........hhhhhhhhhhhhhhhh....eeeeee..........hhhhhhhhhhhhhhhhhhh...eeeeeehhhhhhhhhhhhhhhh.....hhhhhhhhhhhh.eeeeeee....hhhhhhhhh..hhhhhhhhh..hhhhh..hhhhhhhhhhhhhhhhh.eeeeeee.......hhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:-1-261 UniProt: 1-261                                                                                                                                                                                                                                Transcript 1
                 1vkh A  -1 HHmTVRAISPDITLFNKTLTFQEISQNTREAVIYIHGGAWNDPENTPNDFNQLANTIKSmDTESTVCQYSIEYRLSPEITNPRNLYDAVSNITRLVKEKGLTNINmVGHSVGATFIWQILAALKDPQEKmSEAQLQmLGLLQIVKRVFLLDGIYSLKELLIEYPEYDCFTRLAFPDGIQmYEEEPSRVmPYVKKALSRFSIDmHLVHSYSDELLTLRQTNCLISCLQDYQLSFKLYLDDLGLHNDVYKNGKVAKYIFDNIC 261
                              ||    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 
                              ||                                                      60-MSE                                       106-MSE                 130-MSE  |                                        180-MSE  189-MSE       203-MSE                                                      
                              1-MSE                                                                                                                               137-MSE                                                                                                                        
                               4                                                                                                                                                                                                                                                                 


Chain B from PDB  Type:PROTEIN  Length:252
 aligned with KFA_YEAST | Q04066 from UniProtKB/Swiss-Prot  Length:261

    Alignment length:252
                                    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  
            KFA_YEAST    10 PDITLFNKTLTFQEISQNTREAVIYIHGGAWNDPENTPNDFNQLANTIKSMDTESTVCQYSIEYRLSPEITNPRNLYDAVSNITRLVKEKGLTNINMVGHSVGATFIWQILAALKDPQEKMSEAQLQMLGLLQIVKRVFLLDGIYSLKELLVEYPEYDCFTRLAFPDGIQMYEEEPSRVMPYVKKALSRFSIDMHLVHSYSDELLTLRQTNCLISCLQDYQLSFKLYLDDLGLHNDVYKNGKVAKYIFDNIC 261
               SCOP domains d1vkhb_ B: Putative serine hydrolase Ydr428c                                                                                                                                                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....hhhhheeee.......eeeeee..........hhhhhhhhhhhhhhhh....eeeeee..........hhhhhhhhhhhhhhhhhhh...eeeeeehhhhhhhhhhhhhhhh.....hhhhhhhhhhhh.eeeeeee....hhhhhhhhh..hhhhhhhhh..hhhhh..hhhhhhhhhhhhhhhhh.eeeeeee.......hhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
               Transcript 1 Exon 1.1  PDB: B:10-261 UniProt: 1-261 [INCOMPLETE]                                                                                                                                                                                                          Transcript 1
                 1vkh B  10 PDITLFNKTLTFQEISQNTREAVIYIHGGAWNDPENTPNDFNQLANTIKSmDTESTVCQYSIEYRLSPEITNPRNLYDAVSNITRLVKEKGLTNINmVGHSVGATFIWQILAALKDPQEKmSEAQLQmLGLLQIVKRVFLLDGIYSLKELLIEYPEYDCFTRLAFPDGIQmYEEEPSRVmPYVKKALSRFSIDmHLVHSYSDELLTLRQTNCLISCLQDYQLSFKLYLDDLGLHNDVYKNGKVAKYIFDNIC 261
                                    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  
                                                                             60-MSE                                       106-MSE                 130-MSE  |                                        180-MSE  189-MSE       203-MSE                                                      
                                                                                                                                                         137-MSE
   Legend:   → Mismatch (orange background)
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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, 2)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1VKH)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1VKH)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (KFA_YEAST | Q04066)
molecular function
    GO:0004061    arylformamidase activity    Catalysis of the reaction: N-formyl-L-kynurenine + H2O = formate + L-kynurenine.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
biological process
    GO:0034354    'de novo' NAD biosynthetic process from tryptophan    The chemical reactions and pathways resulting in the formation of nicotinamide adenine dinucleotide (NAD), beginning with the synthesis of tryptophan from simpler precursors; biosynthesis may be of either the oxidized form, NAD, or the reduced form, NADH.
    GO:0009435    NAD biosynthetic process    The chemical reactions and pathways resulting in the formation of nicotinamide adenine dinucleotide, a coenzyme present in most living cells and derived from the B vitamin nicotinic acid; biosynthesis may be of either the oxidized form, NAD, or the reduced form, NADH.
    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:0030307    positive regulation of cell growth    Any process that activates or increases the frequency, rate, extent or direction of cell growth.
    GO:0006569    tryptophan catabolic process    The chemical reactions and pathways resulting in the breakdown of tryptophan, the chiral amino acid 2-amino-3-(1H-indol-3-yl)propanoic acid.
    GO:0019441    tryptophan catabolic process to kynurenine    The chemical reactions and pathways resulting in the breakdown of tryptophan into other compounds, including kynurenine.
cellular component
    GO:0005575    cellular_component    The part of a cell, extracellular environment or virus in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.

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