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(-) Description

Title :  CRYSTAL STRUCTURE OF PREDICTED MANDELATE RACEMASE FROM RHODOBACTER SPHAEROIDES
 
Authors :  U. A. Ramagopal, R. Toro, S. C. Almo, S. K. Burley, New York Sgx Resear For Structural Genomics (Nysgxrc)
Date :  08 Aug 06  (Deposition) - 29 Aug 06  (Release) - 01 Feb 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.02
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Structural Genomics, Predicted Mandelate Racemase, Psi, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Nysgxrc, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  U. A. Ramagopal, R. Toro, S. C. Almo
Crystal Structure Of Predicted Mandelate Racemase From Rhodobacter Sphaeroides
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - MANDELATE RACEMASE/MUCONATE LACTONIZING ENZYME/ENOLASE SUPERFAMILY
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: ATCC BAA-808
    Expression System Taxid: 562
    Gene: RSP_3884
    Organism Scientific: RHODOBACTER SPHAEROIDES
    Organism Taxid: 1063

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 7)

Asymmetric/Biological Unit (2, 7)
No.NameCountTypeFull Name
1GOL4Ligand/IonGLYCEROL
2NA3Ligand/IonSODIUM ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:199 , GLU A:227 , GLU A:254 , HIS A:304 , HOH A:1228 , HOH A:1258 , HOH A:1266BINDING SITE FOR RESIDUE NA A 1101
2AC2SOFTWAREASP B:199 , GLU B:227 , GLU B:254 , HOH B:1359 , HOH B:1363BINDING SITE FOR RESIDUE NA B 1102
3AC3SOFTWAREGLY A:174 , HOH A:1366 , HOH A:1396 , HOH A:1400 , HOH B:1423BINDING SITE FOR RESIDUE NA A 1103
4AC4SOFTWAREARG A:249 , ARG A:270 , GLY A:272 , HOH A:1215 , HOH A:1640BINDING SITE FOR RESIDUE GOL A 1201
5AC5SOFTWAREASP B:159 , GLY B:160 , PHE B:161 , TYR B:330BINDING SITE FOR RESIDUE GOL B 1202
6AC6SOFTWAREGLY A:160BINDING SITE FOR RESIDUE GOL A 1203
7AC7SOFTWARELEU B:224 , PHE B:273 , THR B:300 , ALA B:324 , ARG B:326 , ILE B:327 , HOH B:1212BINDING SITE FOR RESIDUE GOL B 1204

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2HZG)

(-) 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:393
 aligned with Q3HKK5_RHOS4 | Q3HKK5 from UniProtKB/TrEMBL  Length:391

    Alignment length:393
                             1                                                                                                                                                                                                                                                                                                                                                                                                   391 
                             |       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       379       389 | 
         Q3HKK5_RHOS4     - -MKIDAVDLFYLSMPEVTDAADGSQDALLVRVAAGGHIGWGECEAAPLPSIAAFVCPKSHGVCRPVSDSVLGQRLDGPDDIARIAALVGYNSMDLLQAPHMLSGIEMALWDLLGRRLSAPAWALLGYSASHGKRPYASLLFGDTPQETLERARAARRDGFAAVKFGWGPIGRGTVAADADQIMAAREGLGPDGDLMVDVGQIFGEDVEAAAARLPTLDAAGVLWLEEPFDAGALAAHAALAGRGARVRIAGGEAAHNFHMAQHLMDYGRIGFIQIDCGRIGGLGPAKRVADAAQARGITYVNHTFTSHLALSASLQPFAGLEADRICEYPAAPQQLALDITGDHIRPDAEGLIRAPEAPGLGLQVAASALRRYLVETEIRIGGQLIYRTPQL-   -
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2hzgA01 A:2-119,A:368-394 Enolase-like, N-terminal domain                                                             2hzgA02 A:120-367 Enolase superfamily                                                                                                                                                                                                                   2hzgA01 A:2-119,A:368-394   CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeee........hhh.eeeeeeeee..eeeeeee..hhhhhhhhhhh........hhhhhh......hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh.hhhhhh........eeeeeee...hhhhhhhhhhhhhhh...eeeee.......hhhhhhhhhhhhhhhhh...eeeee.......hhhhhhhhhhhhhhh...eee......hhhhhhhhhh.....eeee.....hhhhhhhhhhhh...eeeehhhhhhhhhhhhhhhhhhhhhh.eeee....hhhhhhhhhhhhh......eeeee...hhhhhhh.........................hhhhhhhhh..eeeee..eeeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2hzg A   2 SLKIDAVDLFYLSMPEVTDAADGSQDALLVRVAAGGHIGWGECEAAPLPSIAAFVCPKSHGVCRPVSDSVLGQRLDGPDDIARIAALVGYNSMDLLQAPHMLSGIEMALWDLLGRRLSAPAWALLGYSASHGKRPYASLLFGDTPQETLERARAARRDGFAAVKFGWGPIGRGTVAADADQIMAAREGLGPDGDLMVDVGQIFGEDVEAAAARLPTLDAAGVLWLEEPFDAGALAAHAALAGRGARVRIAGGEAAHNFHMAQHLMDYGRIGFIQIDCGRIGGLGPAKRVADAAQARGITYVNHTFTSHLALSASLQPFAGLEADRICEYPAAPQQLALDITGDHIRPDAEGLIRAPEAPGLGLQVAASALRRYLVETEIRIGGQLIYRTPQLE 394
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391   


Chain B from PDB  Type:PROTEIN  Length:391
 aligned with Q3HKK5_RHOS4 | Q3HKK5 from UniProtKB/TrEMBL  Length:391

    Alignment length:391
                             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       379       389 
         Q3HKK5_RHOS4     - -MKIDAVDLFYLSMPEVTDAADGSQDALLVRVAAGGHIGWGECEAAPLPSIAAFVCPKSHGVCRPVSDSVLGQRLDGPDDIARIAALVGYNSMDLLQAPHMLSGIEMALWDLLGRRLSAPAWALLGYSASHGKRPYASLLFGDTPQETLERARAARRDGFAAVKFGWGPIGRGTVAADADQIMAAREGLGPDGDLMVDVGQIFGEDVEAAAARLPTLDAAGVLWLEEPFDAGALAAHAALAGRGARVRIAGGEAAHNFHMAQHLMDYGRIGFIQIDCGRIGGLGPAKRVADAAQARGITYVNHTFTSHLALSASLQPFAGLEADRICEYPAAPQQLALDITGDHIRPDAEGLIRAPEAPGLGLQVAASALRRYLVETEIRIGGQLIYRTPQ 390
               SCOP domains d2hzgb1 B:2-128 automated matches                                                                                              d2hzgb2 B:129-392 automated matches                                                                                                                                                                                                                                      SCOP domains
               CATH domains 2hzgB01 B:2-119,B:368-392 Enolase-like, N-terminal domain                                                             2hzgB02 B:120-367 Enolase superfamily                                                                                                                                                                                                                   2hzgB01 B:2-119,B:368-392 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeee........hhh.eeeeeeeee..eeeeeee..hhhhhhhhhhh........hhhhhh......hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh..hhhhhh........eeeeeee...hhhhhhhhhhhhhhh...eeeee.......hhhhhhhhhhhhhhhhh...eeeee.......hhhhhhhhhhhhhhh...eee......hhhhhhhhhh.....eeee.....hhhhhhhhhhh....eeeehhhhhhhhhhhhhhhhhhhhhh.eeee....hhhhhhhhhhhhh......eee.....hhhhhhh.........................hhhhhhhhh..eeeee..eeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2hzg B   2 SLKIDAVDLFYLSMPEVTDAADGSQDALLVRVAAGGHIGWGECEAAPLPSIAAFVCPKSHGVCRPVSDSVLGQRLDGPDDIARIAALVGYNSMDLLQAPHMLSGIEMALWDLLGRRLSAPAWALLGYSASHGKRPYASLLFGDTPQETLERARAARRDGFAAVKFGWGPIGRGTVAADADQIMAAREGLGPDGDLMVDVGQIFGEDVEAAAARLPTLDAAGVLWLEEPFDAGALAAHAALAGRGARVRIAGGEAAHNFHMAQHLMDYGRIGFIQIDCGRIGGLGPAKRVADAAQARGITYVNHTFTSHLALSASLQPFAGLEADRICEYPAAPQQLALDITGDHIRPDAEGLIRAPEAPGLGLQVAASALRRYLVETEIRIGGQLIYRTPQ 392
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391
   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, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2HZG)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q3HKK5_RHOS4 | Q3HKK5)
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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
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.

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