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(-) Description

Title :  CRYSTAL STRUCTURE OF ATP BOUND RPMATB-BXBCLM CHIMERA B1
 
Authors :  K. C. Rank, H. A. Crosby, J. C. Escalante-Semerena, I. Rayment
Date :  04 Sep 12  (Deposition) - 24 Oct 12  (Release) - 19 Dec 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Keywords :  Rpmatb-Bxbclm Chimera, Anl Superfamily, Methylmalonate-Coa Ligase, Malonate-Coa Ligase, Methylmalonate, Malonate, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. A. Crosby, K. C. Rank, I. Rayment, J. C. Escalante-Semerena
Structural Insights Into The Substrate Specificity Of The Rhodopseudomonas Palustris Protein Acetyltransferase Rppat: Identification Of A Loop Critical For Recognition By Rppat.
J. Biol. Chem. V. 287 41392 2012
PubMed-ID: 23076154  |  Reference-DOI: 10.1074/JBC.M112.417360

(-) Compounds

Molecule 1 - MALONYL COA SYNTHETASE, BENZOATE-COA LIGASE CHIMERIC PROTEIN
    Chains: A, B, C
    EC Number: 6.2.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PTEV5
    Expression System Strain: JE9314
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP Q6ND88 RESIDUES 1-443,466-506 AND UNP Q13WK3 473-497
    Gene: MATB, RPA0221
    Mutation: YES
    Organism Scientific: RHODOPSEUDOMONAS PALUSTRIS, BURKHOLDERIA XENOVORANS
    Organism Taxid: 258594, 266265
    Strain: CGA009, LB400

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): A  
Biological Unit 2 (1x):  B 
Biological Unit 3 (1x):   C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 99)

Asymmetric Unit (4, 99)
No.NameCountTypeFull Name
1ATP3Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2CO33Ligand/IonCARBONATE ION
3MG3Ligand/IonMAGNESIUM ION
4MLY90Mod. Amino AcidN-DIMETHYL-LYSINE
Biological Unit 1 (3, 32)
No.NameCountTypeFull Name
1ATP1Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2CO31Ligand/IonCARBONATE ION
3MG-1Ligand/IonMAGNESIUM ION
4MLY30Mod. Amino AcidN-DIMETHYL-LYSINE
Biological Unit 2 (3, 32)
No.NameCountTypeFull Name
1ATP1Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2CO31Ligand/IonCARBONATE ION
3MG-1Ligand/IonMAGNESIUM ION
4MLY30Mod. Amino AcidN-DIMETHYL-LYSINE
Biological Unit 3 (3, 32)
No.NameCountTypeFull Name
1ATP1Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2CO31Ligand/IonCARBONATE ION
3MG-1Ligand/IonMAGNESIUM ION
4MLY30Mod. Amino AcidN-DIMETHYL-LYSINE

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:163 , SER A:164 , GLY A:165 , THR A:166 , THR A:167 , MLY A:171 , HIS A:207 , SER A:277 , ALA A:278 , PRO A:279 , GLU A:298 , ARG A:299 , GLY A:301 , MET A:302 , THR A:303 , VAL A:322 , ASP A:382 , ARG A:397 , MG A:602 , CO3 A:603 , HOH A:791 , HOH A:814 , HOH A:833 , HOH A:918 , HOH A:941 , HOH A:971 , HOH A:979 , HOH A:982 , HOH A:1016BINDING SITE FOR RESIDUE ATP A 601
2AC2SOFTWAREATP A:601 , HOH A:791 , HOH A:971 , HOH A:979 , HOH A:982BINDING SITE FOR RESIDUE MG A 602
3AC3SOFTWAREHIS A:207 , HIS A:209 , SER A:277 , ARG A:299 , GLY A:301 , ATP A:601BINDING SITE FOR RESIDUE CO3 A 603
4AC4SOFTWARETHR B:163 , SER B:164 , GLY B:165 , THR B:166 , THR B:167 , MLY B:171 , HIS B:207 , SER B:277 , ALA B:278 , PRO B:279 , GLU B:298 , ARG B:299 , GLY B:301 , MET B:302 , THR B:303 , VAL B:322 , ASP B:382 , ARG B:397 , MG B:602 , CO3 B:603 , HOH B:764 , HOH B:807 , HOH B:899 , HOH B:930 , HOH B:1208 , HOH B:1209 , HOH B:1210 , HOH B:1211BINDING SITE FOR RESIDUE ATP B 601
5AC5SOFTWAREATP B:601 , HOH B:1208 , HOH B:1209 , HOH B:1210 , HOH B:1211BINDING SITE FOR RESIDUE MG B 602
6AC6SOFTWAREHIS B:207 , HIS B:209 , SER B:277 , ARG B:299 , GLY B:301 , ATP B:601BINDING SITE FOR RESIDUE CO3 B 603
7AC7SOFTWARETHR C:163 , SER C:164 , GLY C:165 , THR C:166 , THR C:167 , HIS C:207 , SER C:277 , ALA C:278 , PRO C:279 , GLU C:298 , ARG C:299 , GLY C:301 , MET C:302 , THR C:303 , VAL C:322 , ASP C:382 , ARG C:397 , MG C:602 , CO3 C:603 , HOH C:734 , HOH C:795 , HOH C:847 , HOH C:932 , HOH C:936 , HOH C:965 , HOH C:970BINDING SITE FOR RESIDUE ATP C 601
8AC8SOFTWAREATP C:601 , HOH C:734 , HOH C:936 , HOH C:965 , HOH C:970BINDING SITE FOR RESIDUE MG C 602
9AC9SOFTWAREHIS C:207 , SER C:277 , ARG C:299 , GLY C:301 , ATP C:601BINDING SITE FOR RESIDUE CO3 C 603

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4GXQ)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Val A:465 -Mly A:466

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4GXQ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4GXQ)

(-) Exons   (0, 0)

(no "Exon" information available for 4GXQ)

(-) 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:506
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains d4gxqa_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhh.......eeeee....eeehhhhhhhhhhhhhhhhhh......eeeee...hhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhh..eeee...hhhhhhhhhhh...eeee......hhhhhhhhh..............eeeeee.........eeeeehhhhhhhhhhhhhhh......eeee.....hhhhhhhhhhhhhhhh.eeee....hhhhhhhhhhhh.eeeehhhhhhhhhh....hhhhhh...eeee.....hhhhhhhhhhhhh...eeeeee...eeeee...................eeeee.............eeeeee..........hhhhhhhhh.....eeeeeeeee.....eeeeee.hhheee..eeehhhhhhhhhhh...eeeeeeeeeee...eeeeeeeeee......hhhhhhhhhhhh....hhhhh..eeeee...........hhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gxq A   1 MNANLFARLFDkLDDPHkLAIETAAGDkISYAELVARAGRVANVLVARGLQVGDRVAAQTEkSVEALVLYLATVRAGGVYLPLNTAYTLHELDYFITDAEPkIVVCDPSkRDGIAAIAAkVGATVETLGPDGRGSLTDAAAGASEAFATIDRGADDLAAILYTSGTTGRSkGAMLSHDNLASNSLTLVDYWRFTPDDVLIHALPIYHTHGLFVASNVTLFARGSMIFLPkFDPDkILDLMARATVLMGVPTFYTRLLQSPRLTkETTGHMRLFISGSAPLLADTHREWSAkTGHAVLERYGMTETNMNTSNPYDGDRVPGAVGPALPGVSARVTDPETGkELPRGDIGMIEVkGPNVFkGYWRMPEkTkSEFRDDGFFITGDLGkIDERGYVHILGRGkDLVITGGFNVYPkEIESEIDAMPGVVESAVIGVPHADFGEGVTAFVVLkREFAPSEILAEELkAFVkDRLAkFkMPkkVIFVDDLPRNTMGAVQkNVLRETYkDIYk 506
                                    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   |   270       280       290|      300       310       320       330       340       350  |    360      |370       380    |  390       400       410 |     420       430       440       450       460 |   | 470| |  ||480       490   |   500 |   |
                                      12-MLY |        28-MLY                            62-MLY                                 102-MLY 110-MLY   120-MLY                                            171-MLY                                                    230-MLY|                          264-MLY                    291-MLY                                          340-MLY      353-MLY |     367-MLY           385-MLY       399-MLY      412-MLY                             448-MLY       462-MLY    | |  ||              494-MLY 502-MLY
                                            18-MLY                                                                                                                                                                                                                  235-MLY                                                                                                                     359-MLY   369-MLY                                                                                          466-MLY| |  ||                          506-MLY
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                471-MLY||                             
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  473-MLY                             
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     476-MLY                          
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      477-MLY                         


Chain B from PDB  Type:PROTEIN  Length:506
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains d4gxqb_ B: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhh.......eeeee....eeehhhhhhhhhhhhhhhhhh......eeee....hhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhh..eeeehhhhhhhhhhhhhhh..eeee......hhhhhhhhhh.............eeeeee.........eeeeehhhhhhhhhhhhhhh......eeee.....hhhhhhhhhhhhhhhh.eeee....hhhhhhhhhhhh.eeeehhhhhhhhh.....hhhhhh...eeee.....hhhhhhhhhhhhh...eeeeee...eeeee...................eeeee.............eeeeee..........hhhhhhhhh.....eeeeeeeee.....eeeeee.hhheee..eeehhhhhhhhhhhh..eeeeeeeeeee...eeeeeeeeee......hhhhhhhhhhhhh...hhhhh..eeee............hhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gxq B   1 MNANLFARLFDkLDDPHkLAIETAAGDkISYAELVARAGRVANVLVARGLQVGDRVAAQTEkSVEALVLYLATVRAGGVYLPLNTAYTLHELDYFITDAEPkIVVCDPSkRDGIAAIAAkVGATVETLGPDGRGSLTDAAAGASEAFATIDRGADDLAAILYTSGTTGRSkGAMLSHDNLASNSLTLVDYWRFTPDDVLIHALPIYHTHGLFVASNVTLFARGSMIFLPkFDPDkILDLMARATVLMGVPTFYTRLLQSPRLTkETTGHMRLFISGSAPLLADTHREWSAkTGHAVLERYGMTETNMNTSNPYDGDRVPGAVGPALPGVSARVTDPETGkELPRGDIGMIEVkGPNVFkGYWRMPEkTkSEFRDDGFFITGDLGkIDERGYVHILGRGkDLVITGGFNVYPkEIESEIDAMPGVVESAVIGVPHADFGEGVTAFVVLkREFAPSEILAEELkAFVkDRLAkFkMPkkVIFVDDLPRNTMGAVQkNVLRETYkDIYk 506
                                    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   |   270       280       290|      300       310       320       330       340       350  |    360      |370       380    |  390       400       410 |     420       430       440       450       460 |   | 470| |  ||480       490   |   500 |   |
                                      12-MLY |        28-MLY                            62-MLY                                 102-MLY 110-MLY   120-MLY                                            171-MLY                                                    230-MLY|                          264-MLY                    291-MLY                                          340-MLY      353-MLY |     367-MLY           385-MLY       399-MLY      412-MLY                             448-MLY       462-MLY    | |  ||              494-MLY 502-MLY
                                            18-MLY                                                                                                                                                                                                                  235-MLY                                                                                                                     359-MLY   369-MLY                                                                                          466-MLY| |  ||                          506-MLY
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                471-MLY||                             
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  473-MLY                             
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     476-MLY                          
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      477-MLY                         


Chain C from PDB  Type:PROTEIN  Length:506
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains d4gxqc_ C: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhh.......eeeee....eeehhhhhhhhhhhhhhhhhh......eeeee...hhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhh..eeee...hhhhhhhhhhhh..eeee......hhhhhhhhh..............eeeeee.........eeeeehhhhhhhhhhhhhhh......eeee.....hhhhhhhhhhhhhhhh.eeee....hhhhhhhhhhhh.eeeehhhhhhhhhh....hhhhhh...eeee.....hhhhhhhhhhhhh...eeeeee...eeeee...................eeeee.............eeeeee......ee..hhhhhhhhh.....eeeeeeeee.....eeeeee.hhheee..eeehhhhhhhhhhh...eeeeeeeeeee...eeeeeeeeee......hhhhhhhhhhhhh...hhhhh..eeee............hhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gxq C   1 MNANLFARLFDkLDDPHkLAIETAAGDkISYAELVARAGRVANVLVARGLQVGDRVAAQTEkSVEALVLYLATVRAGGVYLPLNTAYTLHELDYFITDAEPkIVVCDPSkRDGIAAIAAkVGATVETLGPDGRGSLTDAAAGASEAFATIDRGADDLAAILYTSGTTGRSkGAMLSHDNLASNSLTLVDYWRFTPDDVLIHALPIYHTHGLFVASNVTLFARGSMIFLPkFDPDkILDLMARATVLMGVPTFYTRLLQSPRLTkETTGHMRLFISGSAPLLADTHREWSAkTGHAVLERYGMTETNMNTSNPYDGDRVPGAVGPALPGVSARVTDPETGkELPRGDIGMIEVkGPNVFkGYWRMPEkTkSEFRDDGFFITGDLGkIDERGYVHILGRGkDLVITGGFNVYPkEIESEIDAMPGVVESAVIGVPHADFGEGVTAFVVLkREFAPSEILAEELkAFVkDRLAkFkMPkkVIFVDDLPRNTMGAVQkNVLRETYkDIYk 506
                                    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   |   270       280       290|      300       310       320       330       340       350  |    360      |370       380    |  390       400       410 |     420       430       440       450       460 |   | 470| |  ||480       490   |   500 |   |
                                      12-MLY |        28-MLY                            62-MLY                                 102-MLY 110-MLY   120-MLY                                            171-MLY                                                    230-MLY|                          264-MLY                    291-MLY                                          340-MLY      353-MLY |     367-MLY           385-MLY       399-MLY      412-MLY                             448-MLY       462-MLY    | |  ||              494-MLY 502-MLY
                                            18-MLY                                                                                                                                                                                                                  235-MLY                                                                                                                     359-MLY   369-MLY                                                                                          466-MLY| |  ||                          506-MLY
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                471-MLY||                             
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  473-MLY                             
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     476-MLY                          
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      477-MLY
   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, 3)

Asymmetric Unit
(-)
Class: Multi-domain proteins (alpha and beta) (2421)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4GXQ)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4GXQ)

(-) Gene Ontology  (9, 13)

Asymmetric Unit(hide GO term definitions)

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  Q6ND88_RHOPA | Q6ND88
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 Related Entries

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

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        Q13WK3_PARXL | Q13WK3: 2v7b 4gxr
        Q6ND88_RHOPA | Q6ND88: 4fuq 4fut 4gxr

(-) Related Entries Specified in the PDB File

2v7b CRYSTAL STRUCTURE OF A BENZOATE COA LIGASE FROM BURKHOLDERIA XENOVORANS LB400
3nyq STRUCTURE OF SCMATB WITH AMP AND METHYLMALONYL-COA BOUND
3nyr STRUCTURE OF SCMATB WITH AMP AND MALONYL-COA BOUND
4fuq STRUCTURE OF APO RPMATB
4fut STRUCTURE OF ATP BOUND RPMATB
4gxr