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(-) Description

Title :  CRYSTAL STRUCTURE OF A PUTATIVE PLP-DEPENDENT BETA-CYSTATHIONASE (AECD, DIP1736) FROM CORYNEBACTERIUM DIPHTHERIAE AT 1.99 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  25 Nov 08  (Deposition) - 09 Dec 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.99
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Plp-Dependent Transferase-Like Fold, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Putative Plp-Dependent Beta-Cystathionase (Np_940074. 1) From Corynebacterium Diphtheriae At 1. 99 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PUTATIVE PLP-DEPENDENT BETA-CYSTATHIONASE
    Chains: A
    EC Number: 3.-.-.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: SPEEDET
    Expression System Strain: HK100
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: AECD, DIP1736, NP_940074.1
    Organism Scientific: CORYNEBACTERIUM DIPHTHERIAE
    Organism Taxid: 1717
    Synonym: BETA C-S LYASE

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 23)

Asymmetric Unit (5, 23)
No.NameCountTypeFull Name
1CL5Ligand/IonCHLORIDE ION
2EDO9Ligand/Ion1,2-ETHANEDIOL
3LLP1Mod. Amino Acid2-LYSINE(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHANE)
4MSE7Mod. Amino AcidSELENOMETHIONINE
5NA1Ligand/IonSODIUM ION
Biological Unit 1 (3, 34)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2EDO18Ligand/Ion1,2-ETHANEDIOL
3LLP2Mod. Amino Acid2-LYSINE(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHANE)
4MSE14Mod. Amino AcidSELENOMETHIONINE
5NA-1Ligand/IonSODIUM ION

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:88 , VAL A:89 , ALA A:219 , SER A:221 , LLP A:222 , HOH A:640BINDING SITE FOR RESIDUE NA A 377
02AC2SOFTWAREPRO A:87 , GLY A:255BINDING SITE FOR RESIDUE CL A 378
03AC3SOFTWAREALA A:30 , ARG A:351 , HOH A:583 , HOH A:596BINDING SITE FOR RESIDUE CL A 379
04AC4SOFTWARECYS A:37 , PRO A:38 , ALA A:39BINDING SITE FOR RESIDUE CL A 380
05AC5SOFTWAREASP A:88 , ARG A:91 , ASP A:254 , GLY A:255 , HOH A:603 , HOH A:663BINDING SITE FOR RESIDUE CL A 381
06AC6SOFTWAREASN A:160 , PRO A:161 , PHE A:342 , ARG A:351BINDING SITE FOR RESIDUE CL A 382
07AC7SOFTWAREPRO A:4 , SER A:5 , ILE A:6 , SER A:357 , GLU A:359BINDING SITE FOR RESIDUE EDO A 383
08AC8SOFTWAREPHE A:196 , VAL A:279 , ALA A:280 , HOH A:433 , HOH A:608 , HOH A:621 , HOH A:810BINDING SITE FOR RESIDUE EDO A 384
09AC9SOFTWAREGLY A:343 , EDO A:391 , HOH A:600BINDING SITE FOR RESIDUE EDO A 385
10BC1SOFTWAREGLU A:173 , ARG A:180 , PRO A:294 , HOH A:731 , HOH A:753BINDING SITE FOR RESIDUE EDO A 386
11BC2SOFTWARETYR A:94 , ILE A:95 , ASP A:98 , HIS A:99 , HOH A:633 , HOH A:802BINDING SITE FOR RESIDUE EDO A 387
12BC3SOFTWAREPHE A:315 , ARG A:316 , THR A:318 , ILE A:320 , GLY A:322BINDING SITE FOR RESIDUE EDO A 388
13BC4SOFTWAREMSE A:15BINDING SITE FOR RESIDUE EDO A 389
14BC5SOFTWARETRP A:341 , HOH A:659BINDING SITE FOR RESIDUE EDO A 390
15BC6SOFTWAREGLY A:343 , GLU A:344 , EDO A:385 , HOH A:610 , HOH A:711BINDING SITE FOR RESIDUE EDO A 391

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Thr A:111 -Pro A:112
2Asn A:157 -Pro A:158
3Asn A:160 -Pro A:161

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3FDB)

(-) 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:377
 aligned with Q6NFZ9_CORDI | Q6NFZ9 from UniProtKB/TrEMBL  Length:376

    Alignment length:377
                             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       279       289       299       309       319       329       339       349       359       369       
         Q6NFZ9_CORDI     - -MQFPSIEDLRARNTMKWTRYGQGVLPLWVAESDFSTCPAVLQAITDAVQREAFGYQPDGSLLSQATAEFYADRYGYQARPEWIFPIPDVVRGLYIAIDHFTPAQSKVIVPTPAYPPFFHLLSATQREGIFIDATGGINLHDVEKGFQAGARSILLCNPYNPLGMVFAPEWLNELCDLAHRYDARVLVDEIHAPLVFDGQHTVAAGVSDTAASVCITITAPSKAWNIAGLKCAQIIFSNPSDAEHWQQLSPVIKDGASTLGLIAAEAAYRYGTDFLNQEVAYLKNNHDFLLHEIPKRIPGAKITPMQATYLMWIDFRDTTIEGSPSEFFIEKAKVAMNDGAWFGEDGTGFCRLNFATSREVLEEAIDRMAKAVSHHT 376
               SCOP domains d3fdba_ A: automated matches                                                                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhh.hhhhhh.....ee..........hhhhhhhhhhhhhh..........hhhhhhhhhhhhhhh...hhh.eeee.hhhhhhhhhhhhhh.....eeeee...hhhhhhhhhhh..eeeee.....hhhhhhhhhhh...eeeee..........hhhhhhhhhhhhhhh..eeeee..hhhhh......hhhhhhhhhhhheeeee.......hhhhh.eeee..hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...ee.......eeeee........hhhhhhhhhhhee.ee.hhhhhhhh.eeeee...hhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fdb A   0 GmQFPSIEDLRARNTmKWTRYGQGVLPLWVAESDFSTCPAVLQAITDAVQREAFGYQPDGSLLSQATAEFYADRYGYQARPEWIFPIPDVVRGLYIAIDHFTPAQSKVIVPTPAYPPFFHLLSATQREGIFIDATGGINLHDVEKGFQAGARSILLCNPYNPLGmVFAPEWLNELCDLAHRYDARVLVDEIHAPLVFDGQHTVAAGVSDTAASVCITITAPSkAWNIAGLKCAQIIFSNPSDAEHWQQLSPVIKDGASTLGLIAAEAAYRYGTDFLNQEVAYLKNNHDFLLHEIPKRIPGAKITPmQATYLmWIDFRDTTIEGSPSEFFIEKAKVAmNDGAWFGEDGTGFCRLNFATSREVLEEAIDRmAKAVSHHT 376
                             |       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       279       289       299     | 309 |     319       329      |339       349       359       369       
                             |            15-MSE                                                                                                                                              164-MSE                                                   222-LLP                                                                            305-MSE |                      336-MSE                         368-MSE    
                             1-MSE                                                                                                                                                                                                                                                                                                               311-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, 1)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q6NFZ9_CORDI | Q6NFZ9)
molecular function
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    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.
    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:0030170    pyridoxal phosphate binding    Interacting selectively and non-covalently with pyridoxal 5' phosphate, 3-hydroxy-5-(hydroxymethyl)-2-methyl4-pyridine carboxaldehyde 5' phosphate, the biologically active form of vitamin B6.
biological process
    GO:0009058    biosynthetic process    The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.

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