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(-) Description

Title :  CRYSTAL STRUCTURE OF A PUTATIVE PHOSPHOENOLPYRUVATE PHOSPHONOMUTASE (NCGL1015, CGL1060) FROM CORYNEBACTERIUM GLUTAMICUM ATCC 13032 AT 1.80 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  05 Jul 07  (Deposition) - 17 Jul 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  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 Pep Phosphonomutase (Np_600288. 1) From Corynebacterium Glutamicum Atcc 13032 Kitasato At 1. 80 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PEP PHOSPHONOMUTASE
    Chains: A, B
    EC Number: 2.7.8.23
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: SPEEDET
    Expression System Strain: HK100
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: NP_600288.1, CGL1060
    Organism Scientific: CORYNEBACTERIUM GLUTAMICUM ATCC 13032
    Organism Taxid: 196627
    Strain: DSM 20300, JCM 1318, LMG 3730, NCIMB 10025

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 26)

Asymmetric/Biological Unit (6, 26)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2GOL11Ligand/IonGLYCEROL
3MSE10Mod. Amino AcidSELENOMETHIONINE
4P6G1Ligand/IonHEXAETHYLENE GLYCOL
5SO42Ligand/IonSULFATE ION
6UNL1Ligand/IonUNKNOWN LIGAND

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETHR A:25 , ASN A:110 , TYR A:185 , THR A:233 , GLY A:235 , GOL A:264 , HOH A:275 , HOH A:289 , HOH A:340BINDING SITE FOR RESIDUE SO4 A 255
02AC2SOFTWARETHR B:25 , ASN B:110 , TYR B:185 , THR B:233 , GLY B:235 , GOL B:258 , HOH B:269 , HOH B:272 , HOH B:286 , HOH B:304BINDING SITE FOR RESIDUE SO4 B 255
03AC3SOFTWAREGOL B:258BINDING SITE FOR RESIDUE CL B 256
04AC4SOFTWAREHIS A:48 , ASP A:58 , PRO A:236 , GOL A:264 , HOH A:344BINDING SITE FOR RESIDUE UNL A 256
05AC5SOFTWARELEU A:221 , HOH A:508 , VAL B:141 , LYS B:251 , TRP B:253 , HOH B:354 , HOH B:469 , HOH B:510BINDING SITE FOR RESIDUE P6G B 257
06AC6SOFTWAREGLY A:215 , ASP A:220 , LEU A:221 , HOH A:348 , HOH A:375 , GLY B:252 , TRP B:253BINDING SITE FOR RESIDUE GOL A 257
07AC7SOFTWARELEU A:20 , LEU A:21 , VAL A:22 , PHE A:40 , SER A:41 , HOH A:324 , HOH A:326 , GLY B:143BINDING SITE FOR RESIDUE GOL A 258
08AC8SOFTWAREGLY A:18 , LEU A:20 , ALA A:225 , GLY A:228 , VAL A:229 , ARG A:230 , GLN B:137BINDING SITE FOR RESIDUE GOL A 259
09AC9SOFTWARELEU A:34 , GLU A:37 , HOH A:338 , ALA B:244 , ALA B:247 , HOH B:351BINDING SITE FOR RESIDUE GOL A 260
10BC1SOFTWAREASP A:140 , GLY A:143 , ASP A:145 , HOH A:345BINDING SITE FOR RESIDUE GOL A 261
11BC2SOFTWAREGLY A:0 , MSE A:1 , SER A:2 , HOH A:358 , ALA B:125 , GLN B:126 , LYS B:171BINDING SITE FOR RESIDUE GOL A 262
12BC3SOFTWARESER A:13 , GLU A:16 , ASP A:145 , ARG A:182 , HOH A:487BINDING SITE FOR RESIDUE GOL A 263
13BC4SOFTWAREARG A:151 , LYS A:156 , TYR A:185 , PRO A:236 , SO4 A:255 , UNL A:256 , HOH A:451 , HOH A:513BINDING SITE FOR RESIDUE GOL A 264
14BC5SOFTWAREARG B:151 , LYS B:156 , TYR B:185 , PRO B:236 , SO4 B:255 , CL B:256 , HOH B:356 , HOH B:387 , HOH B:457BINDING SITE FOR RESIDUE GOL B 258
15BC6SOFTWARESER B:2 , LEU B:4 , LYS B:5 , HOH B:521BINDING SITE FOR RESIDUE GOL B 259
16BC7SOFTWAREMSE B:166 , GLN B:194 , ARG B:197 , HOH B:369 , HOH B:400BINDING SITE FOR RESIDUE GOL B 260

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2QIW)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2QIW)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2QIW)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2QIW)

(-) Exons   (0, 0)

(no "Exon" information available for 2QIW)

(-) 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:255
 aligned with Q8NRI8_CORGL | Q8NRI8 from UniProtKB/TrEMBL  Length:254

    Alignment length:255
                             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     
         Q8NRI8_CORGL     - -MSDLKSLATKFASDHESGKLLVLPTVWDTWSAGLVEEAGFSGLTIGSHPVADATGSSDGENMNFADYMAVVKKITSAVSIPVSVDVESGYGLSPADLIAQILEAGAVGINVEDVVHSEGKRVREAQEHADYIAAARQAADVAGVDVVINGRTDAVKLGADVFEDPMVEAIKRIKLMEQAGARSVYPVGLSTAEQVERLVDAVSVPVNITAHPVDGHGAGDLATLAGLGVRRVTFGPLWQKWLAATSAQQLKGWA 254
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2qiwA01 A:0-235 Phosphoenolpyruvate-binding domains                                                                                                                                                                                         2qiwA02 A:236-254   CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhh...ee..ee.hhhhhhhhhhh....eeehhhhhhhhh........hhhhhhhhhhhhhhhh...eeee.......hhhhhhhhhhhh...eeee...hhhhh....hhhhhhhhhhhhhhhhhhhh...eeeeeehhhhhh.....hhhhhhhhhhhhhhhhh..eeee....hhhhhhhhhh......eee..........hhhhhhhh...eee..hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qiw A   0 GmSDLKSLATKFASDHESGKLLVLPTVWDTWSAGLVEEAGFSGLTIGSHPVADATGSSDGENmNFADYmAVVKKITSAVSIPVSVDVESGYGLSPADLIAQILEAGAVGINVEDVVHSEGKRVREAQEHADYIAAARQAADVAGVDVVINGRTDAVKLGADVFEDPmVEAIKRIKLmEQAGARSVYPVGLSTAEQVERLVDAVSVPVNITAHPVDGHGAGDLATLAGLGVRRVTFGPLWQKWLAATSAQQLKGWA 254
                             |       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     
                             |                                                           62-MSE |                                                                                               166-MSE   176-MSE                                                                          
                             1-MSE                                                             68-MSE                                                                                                                                                                                      


Chain B from PDB  Type:PROTEIN  Length:255
 aligned with Q8NRI8_CORGL | Q8NRI8 from UniProtKB/TrEMBL  Length:254

    Alignment length:255
                             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     
         Q8NRI8_CORGL     - -MSDLKSLATKFASDHESGKLLVLPTVWDTWSAGLVEEAGFSGLTIGSHPVADATGSSDGENMNFADYMAVVKKITSAVSIPVSVDVESGYGLSPADLIAQILEAGAVGINVEDVVHSEGKRVREAQEHADYIAAARQAADVAGVDVVINGRTDAVKLGADVFEDPMVEAIKRIKLMEQAGARSVYPVGLSTAEQVERLVDAVSVPVNITAHPVDGHGAGDLATLAGLGVRRVTFGPLWQKWLAATSAQQLKGWA 254
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2qiwB01 B:0-235 Phosphoenolpyruvate-binding domains                                                                                                                                                                                         2qiwB02 B:236-254   CATH domains
           Pfam domains (1) -----------PEP_mutase-2qiwB01 B:11-254                                                                                                                                                                                                                          Pfam domains (1)
           Pfam domains (2) -----------PEP_mutase-2qiwB02 B:11-254                                                                                                                                                                                                                          Pfam domains (2)
         Sec.struct. author ..hhhhhhhhhhhhhhhh...ee..ee.hhhhhhhhhhh....eeehhhhhhhhh........hhhhhhhhhhhhhhhh...eeee.......hhhhhhhhhhhh...eeee...hhhhh....hhhhhhhhhhhhhhhhhhhh...eeeeeehhhhhh.....hhhhhhhhhhhhhhhh...eeee....hhhhhhhhhh......eee..........hhhhhhhhh..eee..hhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qiw B   0 GmSDLKSLATKFASDHESGKLLVLPTVWDTWSAGLVEEAGFSGLTIGSHPVADATGSSDGENmNFADYmAVVKKITSAVSIPVSVDVESGYGLSPADLIAQILEAGAVGINVEDVVHSEGKRVREAQEHADYIAAARQAADVAGVDVVINGRTDAVKLGADVFEDPmVEAIKRIKLmEQAGARSVYPVGLSTAEQVERLVDAVSVPVNITAHPVDGHGAGDLATLAGLGVRRVTFGPLWQKWLAATSAQQLKGWA 254
                             |       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     
                             1-MSE                                                       62-MSE |                                                                                               166-MSE   176-MSE                                                                          
                                                                                               68-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  (0, 0)

(no "SCOP Domain" information available for 2QIW)

(-) CATH Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: PK_TIM (63)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q8NRI8_CORGL | Q8NRI8)
molecular function
    GO:0008807    carboxyvinyl-carboxyphosphonate phosphorylmutase activity    Catalysis of the reaction: 1-carboxyvinyl carboxyphosphonate = 3-(hydrohydroxyphosphoryl)pyruvate + CO2.
    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:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.

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